Compositions and methods for dengue virus chimeric constructs in vaccines

ABSTRACT

Embodiments herein report compositions, uses and manufacturing of dengue virus constructs and live attenuated dengue viruses. Some embodiments concern a composition that includes, but is not limited to, a tetravalent dengue virus composition. In certain embodiments, compositions can include constructs of one or more serotypes of dengue virus, such as dengue-1 (DEN-1) virus, dengue-2 (DEN-2) virus, dengue-3 (DEN-3) or dengue-4 (DEN-4) virus constructs. In other embodiments, constructs disclosed herein can be combined in a composition to generate a vaccine against more one or more dengue virus constructs that may or may not be subsequently passaged in mammalian cells.

PRIORITY

The instant application is a U.S. divisional application that claimspriority to U.S. Non-Provisional application Ser. No. 14/209,808 filedMar. 13, 2014 which claims the benefit of U.S. Provisional PatentApplication Ser. No. 61/800,204, filed Mar. 15, 2013. These applicationsare incorporated herein by reference in their entirety for all purposes.

FEDERALLY FUNDED RESEARCH

This invention was made with Government support under grant R43AI084291awarded by the National Institutes of Health. The Government has certainrights in this invention.

FIELD

Embodiments herein report compositions, methods, uses and manufacturingprocedures for dengue virus constructs and vaccine compositions thereof.Some embodiments concern a composition that includes, but is not limitedto, chimeric flavivirus virus constructs that alone or in combinationwith other constructs can be used in a vaccine composition. In certainembodiments, compositions can include constructs of more than oneserotypes of dengue virus, such as dengue-1 (DEN-1) virus, dengue-2(DEN-2) virus, dengue-3 (DEN-3) virus and/or dengue-4 (DEN-4) virus. Inother embodiments, manufacturing strategy that can improve the safetyand genetic stability of recombinant live-attenuated chimeric denguevaccine (DENVax) viruses. Certain embodiments include at least one live,attenuated dengue virus in combination with dengue virus chimericconstructs identified to be both safe and effective in vaccinecompositions where the constructs have undergone additional passages incell cultures.

BACKGROUND

Infection with dengue virus can lead to a painful fever of varyingseverity. To date, four serotypes of dengue virus have been identified:dengue-1 (DEN-1), dengue-2 (DEN-2), or dengue-3 (DEN-3) in combinationwith dengue-4 (DEN-4). Dengue fever is caused by infection of a denguevirus. Other subtypes may be discovered in the future (e.g. DEN-5).Dengue virus serotypes 1-4 can also cause dengue hemorrhagic fever(DHF), and dengue shock syndrome (DSS). The most severe consequences ofinfection, DHF and DSS, can be life threatening. Dengue viruses cause50-100 million cases of debilitating dengue fever, 500,000 cases ofDHF/DSS, and more than 20,000 deaths each year. To date, there is noeffective vaccine to protect against dengue fever and no drug treatmentfor the disease. Mosquito control efforts have been ineffective inpreventing dengue outbreaks in endemic areas or in preventing furthergeographic spread of the disease. It is estimated that 3.5 billionpeople are threatened by infection with dengue virus. In addition,dengue virus is a leading cause of fever in travelers to endemic areas,such as Asia, Central and South America, and the Caribbean.

All four dengue virus serotypes are endemic throughout the tropicalregions of the world and constitute the most significant mosquito-borneviral threat to humans in tropical regions, worldwide. Dengue virusesare transmitted to humans primarily by Aedes aegypti mosquitoes.Infection with one dengue virus serotype results in life-long protectionfrom re-infection by that serotype, but does not prevent secondaryinfection by one of the other three dengue virus serotypes. In fact,previous infection with one dengue virus serotype leads to an increasedrisk of severe disease (DHF/DSS) upon secondary infection with adifferent serotype. The development of an effective vaccine representsan important approach to the prevention and control of this globalemerging disease. Multiple immunizations make complete vaccine coveragedifficult both for public health efforts in dengue virus endemiccountries as well as travelers.

SUMMARY

Embodiments herein concern compositions, methods and uses of chimericdengue virus constructs. In some embodiments, a composition can includechimeric dengue virus constructs having an attenuated dengue virusbackbone with structural genes from at least one other dengue virusserotype. Other embodiments concern at least one live, attenuated virusin combination with one or more chimeric dengue viruses. Otherembodiments can include a composition of chimeric dengue viruses havinga modified DEN-2 backbone (e.g. PDK-53 as a starting backbone in P1(passage-1) and passage variability (after passage and growth in vitroon a permissive cell line) as indicated for P2, P3, . . . P8 . . . P10etc.) and one or more structural components of DEN-1, DEN-2, DEN-3 orDEN-4. In other embodiments, an immunogenic composition is generatedwhere when introduced to a subject, the composition produces an immuneresponse to one or more dengue viruses in the subject. Therefore,constructs contemplated herein can be generated and passaged in vitro,and each of the passages provides an attenuated dengue viruscontemplated of use in a pharmaceutically acceptable vaccinecomposition. In certain embodiments a live, attenuated virus can be alive, attenuated dengue-2 virus alone or in combination with one or morechimeric dengue viruses.

In certain examples, chimeric dengue virus constructs of dengue virusserotypes can include passage 7 (P7) live, attenuated viruses orchimeric viruses having nucleic acid sequences identified by SEQ ID NOS:1, 9 , 17, and 25 or polypeptide sequences indicated by SEQ ID NOS: 2,10, 18 and 26. It is contemplated herein that any of the passages forany of the live, attenuated viruses described herein can he used in animmunogenic composition to induce immune responses to the representeddengue viruses (e.g. serotypes 1-4). In accordance with theseembodiments, an immunogenic composition that includes a P-8 isolatedlive, attenuated virus can be administered to a subject to induce animmunogenic response against one or more dengue virus serotypesdepending on the construct selected. In addition, a live, attenuatedvirus can be combined with one or more of these chimeric viruses. Thisis contemplated for each of the live, attenuated virusesisolated/produced in each subsequent cell passages (e.g. African GreenMonkey Vero cell production, hereinafter: Vero cells). It iscontemplated herein that any cell line (e.g. GMP-produced cell bank, FDAor EMA-approved) capable of producing dengue viruses is of use topassage any of the viral constructs at a manufacturing scale or asappropriate contemplated herein for subsequent use in a vaccine orimmunogenic composition against Dengue virus.

In other embodiments, compositions contemplated herein can be combinedwith other immunogenic compositions against other Flaviviruses such asWest Nile virus, Japanese encephalitis or any other flavivirus chimericconstruct and/or live, attenuated virus. In certain embodiments, asingle composition can be used against multiple flaviviruses.

In certain embodiments, an immunogenic composition of the presentinvention can include chimeric dengue viruses against one or more ofDEN-1, DEN-2, DEN-3 and/or DEN-4, alone or in combination with a live,attenuated dengue virus composition.

In other embodiments, a construct can include a construct havingadaptive mutations in the structural or non-structural regions of thevirus that increase growth or production without affecting attenuationor safety of the virus when introduced to a subject. In certainembodiments, any of the contemplated chimeric dengue virus constructscan include a live, attenuated DEN-2 virus having specific mutationsused as a backbone where the live attenuated DEN-2 PDK virus furtherincludes structural proteins of one or more of prM (premembrane) and E(envelope) structural proteins of the other dengue virus serotypes. Inaddition, a DEN-2 backbone can include additional mutations in order toincrease production of or enhance the immune response to a predeterminecomposition in a subject upon administration (e.g. chimeric dengue virus2/1, 2/3 or 2/4).

In some embodiments, structural protein genes can include prM and Egenes of DEN-1, DEN-2, DEN-3 or DEN-4 on a DEN-2 backbone having one ortwo mutations that are part of a live, attenuated dengue virus. Forexample, a dengue construct, in certain embodiments can include thoseconstructs termed DENVax-1-A, DENVax-2-F, DENVax-3-F, and DENVax-4-F(see Example section) where the DEN-2 backbone has one or more mutations(e.g. not found in the P1 or other previous passaged virus or PDK-53)from the DEN-2 live, attenuated virus previously demonstrated to be safeand effective to induce an immune response. The DEN-2 live, attenuatedvirus of the instant application is an improved version of theoriginally used DEN-2 live, attenuated virus. A chimeric construct ofthe instant invention can include a modified attenuated DEN-2 PDK-53backbone, having one or more structural proteins of the second denguevirus serotype wherein the structural proteins can include additionalmutations to increase an immunogenic response to the chimeric construct.In some embodiments, certain mutations acquired by attenuated DEN-2PDK-53 can produce a conservative amino acid change or not in aconstructs different from the P1 construct which can result in desirabletraits for production etc.

In other embodiments, a live, attenuated DEN-2 genome can be used togenerate constructs of dengue virus serotype 1 (DEN-1) and dengue virusserotype 3 (DEN-3), dengue virus serotype 4 (DEN-4) where one or morestructural protein genes of the DEN-2 viral genome can be replaced byone or more structural protein genes of DEN-1, DEN-3 or DEN-4,respectively. In some embodiments, a structural protein can be the C,prM or E protein of a second dengue virus. In certain embodiments,structural protein genes include the prM and E genes of DEN-1, DEN-3 orDEN-4. These hybrid viruses express the surface antigens of DEN-1, DEN-3or DEN-4 while retaining the attenuation phenotypes of the parentattenuated DEN-2.

Constructs disclosed herein can include chimeric constructs of DEN-4,DEN-2, DEN-1, and DEN-3 expressing surface antigens of DEN-1, DEN-3 andDEN-4 using attenuated DEN-2 virus as a backbone.

In certain embodiments, compositions of the instant invention caninclude a composition that comprises a single chimeric dengue virusconstruct disclosed herein and a pharmaceutically acceptable carrier orexcipient. Alternatively, compositions of the instant invention caninclude a composition that comprises two or more, or three or morechimeric dengue virus constructs disclosed herein, and apharmaceutically acceptable carrier or excipient. In accordance withthese embodiments, a one or more dengue virus chimeric constructscontemplated herein can be combined with one or more, live attenuateddengue viruses. In certain embodiments, a live, attenuated virus can bea live, attenuated DEN-2 virus wherein additional mutations in the NCR,NS1 regions or other regions increase the immune response, increaseviral growth or other improvement for an improved live, attenuateddengue virus.

In certain embodiments, the attenuation loci, nucleotide 5′NCR-57-T,NS1-53-Asp, and NS3-250-Val, of the DENV-2 vaccine have been previouslydetermined, and all of these changes are shared by the common PDK-53virus-specific genetic background of the four DENVax viruses. Thegenetic sequence of the three attenuation loci as well as the previouslyestablished in vitro and in vivo attenuation phenotypes of these vaccinecandidates were carefully monitored for the cGMP-manufactured DENVaxseeds. This report describes strategies used to generate master virusseeds (MVS) as well as their genetic and phenotypic characterization ofuse in the manufacture of dengue virus vaccine compositions. These MVScan be used for manufacture of clinical materials and ultimatelycommercial vaccine supplies.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain embodiments. Some embodimentsmay be better understood by reference to one or more of these drawingsalone or in combination with the detailed description of specificembodiments presented.

FIG. 1 represents an exemplary chart reflecting an exemplary chimericconstruct of the instant invention, DEN-2/DEN-4 compared to previouslygenerated constructs and wild type dengue viruses.

FIG. 2 represents an exemplary histogram plot comparing variousresponses using a live, attenuated DEN-2 backbone (with additionalmutations) and a second dengue virus serotype as structural componentssubstituted for the dengue-2 structural components (e.g. DENVax-1 MVS).This plot illustrates plaque sizes of the DENVax MVS. Wild-type Dengueviruses and previously published research-grade vaccine candidateviruses were included for control and comparison. This plot illustratesimproved production of the dengue virus constructs compared to controldengue virus chimeric constructs.

FIG. 3 represents an exemplary histogram plot that representstemperature sensitivities of DENVax MVS (Master Virus Seed). Wild typedengue viruses and previously published research-grade vaccine candidateviruses were included for comparison with the MVS grade.

FIG. 4 represents an exemplary histogram plot that represents viralgrowth of DENVax MVS in C6/36 cells compared to controls. Wild-typedengue viruses and research-grade vaccine candidate viruses wereincluded for comparison with the DENVax MVS.

FIGS. 5A-5C represent exemplary plots of neurovirulence in newborn mice.Pooled results of several experiments summarizing the neurovirulence ofwt DENV-2 16681 virus in CDC-ICR (n=72) and Taconic-ICR (n=32) newbornmice challenged is with 10⁴ pfu of the virus (A). Neurovirulence ofDENVax MVS tested in Taconic-ICR mice with a dose of 10⁴ pfu (B) or 10³pfu (C). The numbers of animals tested per group in one experiment(n=16) or two pooled experiments (n=31 or 32) are indicated.

FIG. 6 represents an exemplary histogram illustrating plaque size of theDENVax MVS, WVS, and BVS. Mean plaque diameters±SD (error bars) of thevirus plaques in Vero or LLC-MK₂ cells under agarose overlay measured onday 9 pi. Wild type DENVs and previously published research-gradevaccine candidate viruses were included for control and comparison.

FIG. 7 represents an exemplary histogram plot illustrating growth ofDENVax MSV, WVS, and BVS in C6/36 cells at two incubation temperaturesto verify their retention of this in vitro attenuation marker afterlarge scale manufacturing.

FIG. 8 represents an exemplary histogram plotting restricted growth ofDENVax MVS, WVS, and BVS in C6/36 cells. Mean titers±SD (error bars) ofthe viruses replicated in C6/36 cells 7 days pi. The wt Dengue virusesand previously published research-grade vaccine candidate viruses wereincluded for comparison.

FIGS. 9A-9B represent exemplary graphs of data of neurovirulence ofDENVax MVS in newborn ICR mice. (A) IC inoculations of the virus at doseof 10⁴ PFU. (B) IC inoculation of the virus at dose of 10³ PFU.

FIG. 10 represents an exemplary chart comparing new live, attenuatedviruses to previously generated live, attenuated dengue viruses.

DEFINITIONS

As used herein, “a” or “an” may mean one or more than one of an item.

As used herein the specification, “subject” or “subjects” may include,but are not limited to, mammals such as humans or mammals, domesticatedor wild, for example dogs, cats, other household pets (e.g. hamster,guinea pig, mouse, rat), ferrets, rabbits, pigs, horses, cattle, prairiedogs, wild rodents, or zoo animals.

As used herein, the terms “virus chimera,” “chimeric virus,” “flaviviruschimera” and “chimeric flavivirus” can mean a construct comprising aportion of the nucleotide sequence of a dengue-2 virus and furthernucleotide sequence that is not from dengue-2 virus or is from adifferent flavivirus. A “dengue chimera” comprises at least twodifferent dengue virus serotypes but not a different flavivirus. Thus,examples of other dengue viruses or flaviviruses include, but are notlimited to, sequences from dengue-1 virus, dengue-3 virus, dengue-4virus, West Nile virus, Japanese encephalitis virus, St. Louisencephalitis virus, tick-borne encephalitis virus, yellow fever virusand any combination thereof.

As used herein, “nucleic acid chimera” can mean a construct of theinvention comprising nucleic acid comprising a portion of the nucleotidesequence of a dengue-2 virus and further nucleotide sequence that is notof the same origin as the nucleotide sequence of the dengue-2 virus.Correspondingly, any chimeric flavivirus or flavivirus chimera disclosedherein can be recognized as an example of a nucleic acid chimera.

As used herein, “a live, attenuated virus” can mean a wild-type virus,mutated or selected for traits of use in vaccine or other immunogeniccompositions wherein some traits can include reduced virulence, safety,efficacy or improved growth etc.

DESCRIPTION

In the following sections, various exemplary compositions and methodsare described in order to detail various embodiments. It will be obviousto one skilled in the art that practicing the various embodiments doesnot require the employment of all or even some of the specific detailsoutlined herein, but rather that concentrations, times and otherspecific details may be modified through routine experimentation. Insome cases, well-known methods or components have not been included inthe description.

In accordance with embodiments of the present invention, there may beemployed conventional molecular biology, protein chemistry,microbiology, and recombinant DNA techniques within the skill of theart. Such techniques are explained fully in the literature. See, e.g.,Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual,Second Edition 1989, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y.; Animal Cell Culture, R. I. Freshney, ed., 1986).

Embodiments herein concern compositions, methods and uses for inducingimmune responses against one or more dengue virus serotypes in asubject, individually or simultaneously. In accordance with theseembodiments, attenuated dengue viruses and nucleic acid chimeras aregenerated and used in vaccine compositions disclosed herein. Someembodiments concern modified or mutated dengue constructs or chimeras.Other embodiments concern introducing mutations to modify the amino acidsequences of structural proteins of dengue viruses wherein the mutationincrease immunogenicity to the virus.

Live, attenuated dengue viruses of all four serotypes have beendeveloped by passaging wild-type viruses in cell culture. These are someof the most promising live, attenuated vaccine candidates forimmunization against flavivirus and in particular dengue virus infectionand/or disease. These vaccine candidates have been designated by acombination of their dengue serotype, the cell line through which theywere passaged and the number of times they were passaged. Thus, a dengueserotype 1 wild-type virus passaged in PDK cells 13 times is designatedas DEN-1 PDK-13 virus. Other vaccine candidates are DEN-2 PDK-53, DEN-3PGMK-30/FRhL-3 (e.g. thirty passages in primary green monkey kidneycells, followed by three passages in fetal rhesus lung cells and DEN-4PDK-48). These four candidate vaccine viruses were derived by tissueculture passage of wild-type parental DEN-1 16007, DEN-2 16681, DEN-316562 and DEN-4 1036 viruses, respectively.

In certain embodiments, live, attenuated dengue-2 PDK-53 vaccine viruscontained a mixture of viruses, with the population containing varyingnucleotide differences. After genetic characterization of theattenuating mutations, certain attenuating characteristics were outlinedand engineered into a cDNA infectious clone. RNA was transcribed fromthis infectious clone and introduced into Vero cells as a passage 1 ofthe newly characterized and derived PDK-53-Vero-DEN-2-P 1 virus (see forexample, Table 1). This attenuated virus was created for each DENserotype, but for DEN-1, DEN-3 and DEN-4, the prM and E genes wereengineered into 3 separate cDNA infectious clones, thus generating fourseparate PDK-53-Vero viruses (termed herein as: PDK-53-Vero-DEN-2-P 1,PDK-53-Vero-DEN-1-P 1, PDK-53-Vero-DEN-3-P 1, and PDK-53-Vero-DEN-4-P1). These attenuated vaccine virus strains were passaged in Vero cells10 times (Table 1), and each separate lineage acquired mutations upontheir adaptation to grow in Vero cells (Table 3). Certain embodimentshere are directed to derivation and uses for these live, attenuateddengue viruses.

Previous human clinical trials with these attenuated viruses haveindicated that DEN-2 PDK-53 has the lowest infectious dose (50% minimalinfectious dose of 5 plaque forming units or PFU) in humans, is stronglyimmunogenic, and produces no apparent safety concerns. The DEN-1 PDK-13,DEN-3 PGMK-30/FRhL-3 and DEN-4 PDK-48 vaccine virus candidates havehigher 50% minimal infectious doses of 10,000, 3500, and 150 PFU,respectively, in humans. Although only one immunization with monovalentDEN-2 PDK-53 virus or DEN-4 PDK-48 virus was required to achieve 100%seroconversion in human subjects, a booster was needed to achieve thesame seroconversion rate for DEN-1 PDK-13 and DEN-3 PGMK-30/FRhL-3viruses, which have the two highest infectious doses for humans.

DEN-2 PDK-53 virus vaccine candidate, also abbreviated PDK-53, hasseveral measurable biological markers associated with attenuation,including temperature sensitivity, small plaque size, decreasedreplication in mosquito C6136 cell culture, decreased replication inintact mosquitoes, loss of neurovirulence for suckling mice anddecreased incidence of viremia in monkeys. Clinical trials of thecandidate PDK-53 vaccine have demonstrated its safety and immunogenicityin humans. Furthermore, the PDK-53 vaccine induces dengue virus-specificT-cell memory responses in human vaccine recipients. Some embodimentsherein describe an improvement on the DEN-2 PDK-53 used in chimericconstructs disclosed herein.

Immunogenic flavivirus chimeras having a dengue-2 virus backbone and atleast one structural protein of another dengue virus serotype can beused for preparing the dengue virus chimeras and methods for producingthe dengue virus chimeras are described. The immunogenic dengue viruschimeras are provided, alone or in combination, in a pharmaceuticallyacceptable carrier as immunogenic compositions to minimize, inhibit, orimmunize individuals against infection by one or more serotypes, such asdengue virus serotypes DEN-1, DEN-2, DEN-3 and DEN-4, alone or incombination. When combined, the immunogenic dengue virus chimeras may beused as multivalent vaccines (e.g. bi-, tri- and tetravalent) to confersimultaneous protection against infection by more than one species orstrain of flavivirus. In certain embodiments, the dengue virus chimerasare combined in an immunogenic composition useful as a bivalent,trivalent or tetravalent vaccine against the known dengue virusserotypes or confer immunity to other pathogenic flaviviruses byincluding nucleic acids encoding one or more proteins from a differentflavivirus.

In some embodiments, avirulent, immunogenic dengue virus chimerasprovided herein contain the nonstructural protein genes of theattenuated dengue-2 virus (e.g. PDK-53), or the equivalent thereof, andone or more of the structural protein genes or immunogenic portionsthereof of the flavivirus against which immunogenicity is to be inducedin a subject. For example, some embodiments concern a chimera havingattenuated dengue-2 virus PDK-53 genome as the viral backbone, and oneor more structural protein genes encoding capsid, premembrane/membrane,or envelope of the PDK-53 genome, or combinations thereof, replaced withone or more corresponding structural protein genes from DEN-1, DEN-3 orDEN-4 or other flavivirus to be protected against, such as a differentflavivirus or a different dengue virus serotype. In accordance withthese embodiments, a nucleic acid chimera disclosed herein can havefunctional properties of the attenuated dengue-2 virus and is avirulent,but expresses antigenic epitopes of the structural gene products ofDEN-1, DEN-3 or DEN-4 in addition to other flaviviruses and isimmunogenic (e.g. induces an immune response to the gene products in asubject). Then, these DNA constructs are used to transcribe RNA from aninfectious clone, this RNA is introduced into Vero cells again producinga new progeny virus at P1. These new progeny viruses are distinguishablefrom PDK-53. (See e.g. P1-P10).

In another embodiment, a nucleic acid chimera can be a nucleic acidchimera having, but not limited to, a first nucleotide sequence encodingnonstructural proteins from an attenuated dengue-2 virus, and a secondnucleotide sequence encoding a structural protein from dengue-4 virusalone or in combination with another flavivirus. In other embodiments,the attenuated dengue-2 virus can be vaccine strain PDK-53 having one ormore mutated amino acids (see Examples). These additional mutationsconfer desirable traits of use as live, attenuated dengue-2 or aschimeric constructs described herein. Some embodiments includestructural proteins of one or more of C, prM or E protein of a seconddengue virus.

Other aspects include that chimeric viruses can include nucleotide andamino acid substitutions, deletions or insertions for example, in thecontrol PDK-53 dengue-2 genome to reduce interference withimmunogenicity responses to a targeted dengue virus serotype. Thesemodifications can be made in structural and nonstructural proteins aloneor in combination with the example modifications disclosed herein andcan be generated by passaging the attenuated virus and obtaining animproved composition for inducing an immune response against one or moredengue virus serotypes.

Certain embodiments disclosed herein provide for method for making thechimeric viruses of this invention using recombinant techniques, byinserting the required substitutions into the appropriate backbonegenome. Other embodiments herein concern passaging a confirmed (e.g.safe and effective) live, attenuated chimeric virus for additionalimprovements. In certain embodiments, a dengue-2 backbone used hereincan include one or more mutations presented in Table 3. In otherembodiments, a dengue-dengue chimera of the instant application caninclude one or more mutations as presented in Table 3. In yet otherembodiments, a dengue-dengue chimera can include all of the mutationsfor each chimera as represented in Table 3 for Den-2/Den-1, Den-2/Den-3or Den-2/Den-4. Pharmaceutical compositions that include a live,attenuated virus represented by the constructs of Table 3 arecontemplated. For example, mono-, di-, tri- or tetravalent compositionsare contemplated of use herein using chimeras and live, attenuateddengue-2 viruses as presented in Table 3.

In certain embodiments, a live, attenuated DEN-2 variant contemplatedherein can be formulated into a pharmaceutical composition wherein thepharmaceutical composition can be administered alone or in combinationwith dengue-dengue chimeras or dengue-flavivirus chimeras. In certainembodiments, a bi-, tri or tetravalent compositions can be administeredin a single application or in multiple applications to a subject.

Flavivirus Chimeras

Dengue virus types 1-4 (DEN-1 to DEN-4) are mosquito-borne flaviviruspathogens. The flavivirus genome contains a 5′-noncoding region (5′-NC),followed by a capsid protein (C) encoding region, followed by apremembrane/membrane protein (prM) encoding region, followed by anenvelope protein (E) encoding region, followed by the region encodingthe nonstructural proteins (NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5) and finallya 3′ noncoding region (3′NC). The viral structural proteins are C, prMand E, and the nonstructural proteins are NS1-NS5. The structural andnonstructural proteins are translated as a single polyprotein andprocessed by cellular and viral proteases.

Flavivirus chimeras can be constructs formed by fusing non-structuralprotein genes from one type, or serotype, of dengue virus or virusspecies of the flaviviridae, with protein genes, for example, structuralprotein genes, from a different type, or serotype, of dengue virus orvirus species of the flaviviridae. Alternatively, a flavivirus chimeraof the invention is a construct formed by fusing non-structural proteingenes from one type, or serotype, of dengue virus or virus species ofthe flaviviridae, with further nucleotide sequences that direct thesynthesis of polypeptides or proteins selected from other dengue virusserotypes or other viruses of the flaviviridae.

In other embodiments, avirulent, immunogenic flavivirus chimerasprovided herein contain the nonstructural protein genes of theattenuated dengue-2 virus, or the equivalent thereof, and one or more ofthe structural protein genes, or antigenic portions thereof, of theflavivirus against which immunogenicity is to be conferred. Suitableflaviviruses include, but are not limited to those listed in Table 1.

Other suitable dengue viruses for use in constructing the chimeras canbe wild-type, virulent DEN-1 16007, DEN-2 16681, DEN-3 16562 and DEN-41036 and attenuated, vaccine-strain DEN-1 PDK-13, DEN-2 PDK-53, DEN-3PMK-30/FRhL-3 and DEN-4 PDK-48. Genetic differences between the DEN-1,DEN-2, DEN-3 and DEN-4 wild type/attenuated virus pairs are contemplatedalong with changes in the amino acid sequences encoded by the viralgenomes.

Sequence listings for DEN-2 PDK-53 correspond to the DEN-2 PDK-53-Vvariant, wherein genome nucleotide position 5270 is mutated from an A toa T and amino acid position 1725 of the polyprotein or amino acidposition 250 of the NS3 protein contains a valine residue. The DEN-2PDK-53 variant without this nucleotide mutation, DEN-2 PDK-53-E, differsfrom PDK-53-V only in this one position. DEN-2 PDK-53-E has an A atnucleotide position 5270 and a glutamate at polyprotein amino acidposition 1725, NS3 protein amino acid position 250. It is understoodthat embodiments herein include modified PDK 53 that include one or morepassages in a separate host cell (e.g. Vero cells, see Table 1) wheredesirable traits of use in vaccine compositions contemplated herein aregenerated.

In certain embodiments, designations of the chimeras can be based on theDEN-2 virus-specific infectious clone modified backbones and structuralgenes (prM-E or C-prM-E) insert of other dengue viruses or otherflaviviruses. DEN-2 for the dengue-2 backbone, followed by the strainfrom which the structural genes are inserted. One DEN-2 backbone variantis reflected in the next letter after the number designation. Oneparticular DEN-2 backbone variant from which the chimera was constructedis indicated by the following letter placed after a hyphen, parent 16681(P), PDK-53-E (E), or PDK-53-V (V); the last letter indicates theC-prM-E structural genes from the parental (P) strain or its vaccinederivative (V) or the prM-E structural genes from the parental (P) orits vaccine derivative (V1). For example; DEN-2/1-VP denotes the chimeracomprising the attenuated DEN-2 PDK-53V backbone comprising a valine atNS3-250 and the C-prM-E genes from wild-type DEN-1 16007; DEN-2/1-VVdenotes the DEN-2 PDK-53V backbone with the vaccine strain of dengue-1,DEN-1 PDK-13; DEN-2/1-VP1 denotes the DEN-2 PDK-53V backbone and theprM-E genes from wild-type DEN-1 16007; DEN-2/3-VP1 denotes the DEN-2PDK-53V backbone and the prM-E genes from wild-type DEN-3 16562;DEN-2/4VP1 denotes the DEN-2 PDK-53V backbone and the prM-E genes fromwild-type DEN-4 1036. Other chimeras disclosed herein are indicated bythe same manner.

In one embodiment, chimeras disclosed herein contain attenuated dengue-2virus PDK-53 genome as the viral backbone, in which the structuralprotein genes encoding C, prM and E proteins of the PDK-53 genome, orcombinations thereof, can be replaced with the corresponding structuralprotein genes from dengue-1, dengue-3 or dengue-4 virus and optionally,another flavivirus to be protected against, such as a differentflavivirus or a different dengue virus strain.

In the nonstructural protein regions, a Gly-to-Asp (wild type-to-PDK-53)mutation was discovered at nonstructural protein NS1-53 (genomenucleotide position 2579); a Leu-to-Phe (wild type-to-PDK-53) mutationwas discovered at nonstructural protein NS2A-181 (genome nucleotideposition 4018); a Glu-to-Val (wild type-to-PDK-53) mutation wasdiscovered at nonstructural protein NS3-250 (genome nucleotide position5270); and a Gly-to-Ala mutation (wild type-to-PDK-53) was discovered atnonstructural protein NS4A-75 (genome nucleotide position 6599). Thelive, attenuated DEN-2 virus of the instant invention further includesmutations as presented in any chimera or live, attenuated dengue-2 virusof Table 3.

PDK-53 virus strain has a mixed genotype at genome nucleotide 5270. Asignificant portion (approximately 29%) of the virus population encodesthe non-mutated NS3-250-Glu that is present in the wild type DEN-2 16681virus rather than the NS3-250-Val mutation. As both genetic variants areavirulent, this mutation may not be necessary in an avirulent chimera.

Previously, it was discovered that avirulence of the attenuated PDK-53virus strain can be attributed to mutations in the nucleotide sequenceencoding nonstructural proteins and in the 5′ noncoding region. Forexample, a single mutation at NS1-53, a double mutation at NS1-53 and at5′NC-57, a double mutation at NS1-53 and at NS3-250 and a triplemutation at NS1-53, at 5′NC-57 and at NS3-250, result in attenuation ofthe DEN-2 virus. Therefore, the genome of any dengue-2 virus containingsuch non-conservative amino acid substitutions or nucleotidesubstitutions at these loci can be used as a base sequence for derivingthe modified PDK-53 viruses disclosed herein. Another mutation in thestem of the stem/loop structure in the 5′ noncoding region will provideadditional avirulent phenotype stability, if desired. Mutations to thisregion disrupt potential secondary structures important for viralreplication. A single mutation in this short (only 6 nucleotide residuesin length) stem structure in both DEN and Venezuelan equine encephalitisviruses disrupts the formation of the hairpin structure. Furthermutations in this stem structure decrease the possibility of reversionat this locus, while maintaining virus viability.

Mutations disclosed herein can be achieved by any method known in theart including, but not limited to, naturally-occurring or selectedclones having additional features once passaged in a cell line ofinterest (e.g. Vero cells). It is understood by those skilled in the artthat the virulence screening assays, as described herein and as are wellknown in the art, can be used to distinguish between virulent andavirulent backbone structures.

Construction of Flavivirus Chimeras

Flavivirus chimeras described herein can be produced by splicing one ormore of the structural protein genes of the flavivirus against whichimmunity is desired into a PDK-53 dengue virus genome backbone, or othermethods known in the art, using recombinant engineering to remove thecorresponding PDK-53 gene and replace it with a dengue-1, dengue-3 ordengue-4 virus gene or other gene known in the art.

Alternatively, using the sequences provided in the sequence listing, thenucleic acid molecules encoding the flavivirus proteins may besynthesized using known nucleic acid synthesis techniques and insertedinto an appropriate vector. Avirulent, immunogenic virus is thereforeproduced using recombinant engineering techniques known to those skilledin the art.

A target gene can be inserted into the backbone that encodes aflavivirus structural protein of interest for DEN-1, DEN-3, DEN-4 orother flavivirus. A flavivirus gene to be inserted can be a geneencoding a C protein, a PrM protein and/or an E protein. The sequenceinserted into the dengue-2 backbone can encode both PrM and E structuralproteins. The sequence inserted into the dengue-2 backbone can encodeall or one of C, prM and E structural proteins.

Suitable chimeric viruses or nucleic acid chimeras containing nucleotidesequences encoding structural proteins of other flaviviruses or denguevirus serotypes can be evaluated for usefulness as vaccines by screeningthem for the foregoing phenotypic markers of attenuation that indicateavirulence and by screening them for immunogenicity. Antigenicity andimmunogenicity can be evaluated using in vitro or in vivo reactivitywith flavivirus antibodies or immunoreactive serum using routinescreening procedures known to those skilled in the art.

Dengue Virus Vaccines

In certain embodiments, chimeric viruses and nucleic acid chimeras canprovide live, attenuated viruses useful as immunogens or vaccines. Someembodiments include chimeras that exhibit high immunogenicity todengue-4 virus while producing no dangerous pathogenic or lethaleffects.

To reduce occurrence of DHF/DSS in subjects, a tetravalent vaccine isneeded to provide simultaneous immunity for all four serotypes of thevirus. A tetravalent vaccine is produced by combining a live, attenuateddengue-2 virus of the instant application with dengue-2/1, dengue-2/3,and dengue-2/4 chimeras described above in a suitable pharmaceuticalcarrier for administration as a multivalent vaccine.

The chimeric viruses or nucleic acid chimeras of this invention caninclude structural genes of either wild-type or live, attenuated virusin a virulent or an attenuated DEN-2 virus backbone. For example, thechimera may express the structural protein genes of wild-type DEN-4 1036virus, its candidate vaccine derivative in either DEN-2 backgrounds.

Viruses used in the chimeras described herein can be grown usingtechniques known in the art. Virus plaque titrations are then performedand plaques counted in order to assess the viability and phenotypiccharacteristics of the growing cultures. Wild type viruses can bepassaged through cultured cell lines to derive attenuated candidatestarting materials.

Chimeric infectious clones can be constructed from the various dengueserotype clones available. The cloning of virus-specific cDNA fragmentscan also be accomplished, if desired. The cDNA fragments containing thestructural protein or nonstructural protein genes are amplified byreverse transcriptase-polymerase chain reaction (RT-PCR) from denguevirus RNA with various primers Amplified fragments are cloned into thecleavage sites of other intermediate clones. Intermediate, chimericdengue virus clones are then sequenced to verify the accuracy of theinserted dengue virus-specific cDNA.

Full genome-length chimeric plasmids constructed by inserting thestructural protein and/or nonstructural protein gene region of dengueserotype viruses into vectors are obtainable using recombinanttechniques well known to those skilled in the art.

Nucleotide and Amino Acid Analysis

The NS1-53 mutation in the DEN-2 PDK-53 vaccine virus is significant forthe attenuated phenotype of this virus, because the NS1-53-Gly of theDEN-2 16681 virus is conserved in nearly all flaviviruses, including thetick-borne viruses, sequenced to date. DEN-4 vaccine virus can alsocontain an amino acid mutation in the NS1 protein at position 253. Thislocus, which is a Gln-to-His mutation in DEN-4 PDK-48 vaccine virus, isGln in all four wild serotypes of dengue virus. This Gln residue isunique to the dengue viruses within the flavivirus genus. The NS1protein is a glycoprotein that is secreted from flavivirus-infectedcells. It is present on the surface of the infected cell andNS1-specific antibodies are present in the serum of virus-infectedindividuals. Protection of animals immunized with NS1 protein orpassively with NS1-specific antibody has been reported. The NS1 proteinappears to participate in early viral RNA replication.

The mutations that occurred in the NS2A, NS2B, NS4A, and NS4B proteinsof the DEN-1, -2, -3 and -4 attenuated strains are conservative innature. The NS4A-75 and NS4A-95 mutations of DEN-2 and DEN-4 vaccineviruses, respectively, occurred at sites of amino acid conservationamong dengue viruses, but not among flaviviruses in general.

The flaviviral NS3 protein possesses at least two recognized functions:the viral proteinase and RNA helicase/NTPase. The 698-aa long (DEN-2virus) NS3 protein contains an amino-terminal serine protease domain(NS3-51-His, -75-Asp, -135-Ser catalytic triad) that is followed bysequence motifs for RNA helicase/NTPase functions (NS3-196-GAGKT-284-DEAH, -459-GRIGR). None of the mutations in the NS3 proteins ofDEN-1, DEN-2, or DEN-3 virus occurred within a recognized motif. TheNS3-510 Tyr-to-Phe mutation in DEN-1 PDK-13 virus was conservative.Since the wild-type DEN-2, -3 and -4 viruses contain Phe at thisposition, it is unlikely that the Tyr-to-Phe mutation plays a role inthe attenuation of DEN-1 virus. The NS3-182 Glu-to-Lys mutation in DEN-1PDK-13 virus occurred at a position that is conserved as Asp or Glu inmost mosquito-borne flaviviruses and it may play some role inattenuation. This mutation was located 15 amino acid residues upstreamof the GAGKT helicase motif. As noted in previous reports, theNS3-250-Glu in DEN-2 16681 virus is conserved in all mosquito-borneflaviviruses except for yellow fever virus.

Nucleic acid probes selectively hybridize with nucleic acid moleculesencoding the DEN-1, DEN-3 and DEN-4 viruses or complementary sequencesthereof. By “selective” or “selectively” is meant a sequence which doesnot hybridize with other nucleic acids to prevent adequate detection ofthe dengue virus. Therefore, in the design of hybridizing nucleic acids,selectivity will depend upon the other components present in a sample.The hybridizing nucleic acid should have at least 70% complementaritywith the segment of the nucleic acid to which it hybridizes. As usedherein to describe nucleic acids, the term “selectively hybridizes”excludes the occasional randomly hybridizing nucleic acids, and thus,has the same meaning as “specifically hybridizing.” The selectivelyhybridizing nucleic acid of this invention can have at least 70%, 80%,85%, 90%, 95%, 97%, 98%, and 99% complementarity with the segment of thesequence to which it hybridizes, preferably 85% or more.

Sequences, probes and primers which selectively hybridize to theencoding nucleic acid or the complementary, or opposite, strand of thenucleic acid are contemplated. Specific hybridization with nucleic acidcan occur with minor modifications or substitutions in the nucleic acid,so long as functional species-specific hybridization capability ismaintained. By “probe” is meant nucleic acid sequences that can be usedas probes or primers for selective hybridization with complementarynucleic acid sequences for their detection or amplification, whichprobes can vary in length from about 5 to 100 nucleotides, or preferablyfrom about 10 to 50 nucleotides, or most preferably about 18-24nucleotides.

If used as primers, the composition preferably includes at least twonucleic acid molecules which hybridize to different regions of thetarget molecule so as to amplify a desired region. Depending on thelength of the probe or primer, the target region can range between 70%complementary bases and full complementarity and still hybridize understringent conditions. For example, for the purpose of detecting thepresence of the dengue virus, the degree of complementarity between thehybridizing nucleic acid (probe or primer) and the sequence to which ithybridizes is at least enough to distinguish hybridization with anucleic acid from other organisms.

Nucleic acid sequences encoding the DEN-4, DEN-3 or DEN-1 virus (e.g.structural elements) can be inserted into a vector, such as a plasmid,and recombinantly expressed in a living organism (e.g. into a dengue-2backbone) to produce recombinant dengue virus peptides and/orpolypeptides and/or viruses.

Nucleic Acid Detection Methods

A rapid genetic test that is diagnostic for each of the vaccine virusesdescribed herein is provided by the current invention. This embodimentof the invention enhances analyses of viruses isolated from the serum ofvaccinated humans who developed a viremia, as well as enhancingcharacterization of viremia in nonhuman primates immunized with thecandidate vaccine viruses.

These sequences include a diagnostic TaqMan probe that serves to reportthe detection of the cDNA amplicon amplified from the viral genomic RNAtemplate by using a reverse-transciptase/polymerase chain reaction(RT/PCR), as well as the forward and reverse amplimers that are designedto amplify the cDNA amplicon, as described below. In certain instances,one of the amplimers has been designed to contain a vaccinevirus-specific mutation at the 3′-terminal end of the amplimer, whicheffectively makes the test even more specific for the vaccine strainbecause extension of the primer at the target site, and consequentlyamplification, will occur only if the viral RNA template contains thatspecific mutation.

Automated PCR-based nucleic acid sequence detection system can be used,or other known technology for nucleic acid detection. The TaqMan assayis a highly specific and sensitive assay that permits automated, realtime visualization and quantitation of PCR-generated amplicons from asample nucleic acid template. TaqMan can determine the presence orabsence of a specific sequence. In this assay, a forward and a reverseprimer are designed to anneal upstream and downstream of the targetmutation site, respectively. A specific detector probe, which isdesigned to have a melting temperature of about 10.degree.C. higher thaneither of the amplimers and containing the vaccine virus-specificnucleotide mutation or its complement (depending on the strand of RT/PCRamplicon that is being detected), constitutes the third primer componentof this assay.

A probe designed to specifically detect a mutated locus in one of thevaccine viral genomes will contain the vaccine-specific nucleotide inthe middle of the probe. This probe will result in detectablefluorescence in the TaqMan assay if the viral RNA template is vaccinevirus-specific. However, genomic RNA templates from wild-type DENviruses will have decreased efficiency of probe hybridization because ofthe single nucleotide mismatch (in the case of the parental viruses DENviruses) or possibly more than one mismatch (as may occur in otherwild-type DEN viruses) and will not result in significant fluorescence.The DNA polymerase is more likely to displace a mismatched probe fromthe RT/PCR amplicon template than to cleave the mismatched probe torelease the reporter dye (TaqMan Allelic Discrimination assay, AppliedBiosystems).

One strategy for diagnostic genetic testing makes use of molecularbeacons. The molecular beacon strategy also utilizes primers for RT/PCRamplification of amplicons, and detection of a specific sequence withinthe amplicon by a probe containing reporter and quencher dyes at theprobe termini. In this assay, the probe forms a stem-loop structure. Themolecular beacons assay employs quencher and reporter dyes that differfrom those used in the TaqMan assay.

Pharmaceutical Compositions

Embodiments herein provide for administration of compositions tosubjects in a biologically compatible form suitable for pharmaceuticaladministration in vivo. By “biologically compatible form suitable foradministration in vivo” is meant a form of the active agent (e.g.pharmaceutical chemical, protein, gene, of the embodiments) to beadministered in which any toxic effects are outweighed by thetherapeutic effects of the active agent. Administration of atherapeutically active amount of the therapeutic compositions is definedas an amount effective, at dosages and for periods of time necessary toachieve the desired result. For example, a therapeutically active amountof a compound may vary according to factors such as the disease state,age, sex, and weight of the individual, and the ability of antibody toelicit a desired response in the individual. Dosage regima may beadjusted to provide the optimum therapeutic response.

In one embodiment, the compound (e.g. pharmaceutical chemical, protein,peptide etc. of the embodiments) may be administered in a convenientmanner, for example, subcutaneous, intravenous, by oral administration,inhalation, intradermal, transdermal application, intravaginalapplication, topical application, intranasal or rectal administration.Depending on the route of administration, the active compound may becontained in a protective buffer (e.g. FTA, F127/trehalose/albumin) Inone embodiment, a composition may be orally administered. In anotherembodiment, the composition may be administered intravenously. In oneembodiment, the composition may be administered intranasally, such asinhalation. In yet another embodiment, the composition may beadministered intradermally using a needle-free system (e.g. Pharmajet®)or other intradermal administration system.

A composition may be administered to a subject in an appropriate carrieror diluent, co-administered with enzyme inhibitors or in an appropriatecarrier such as liposomes. The term “pharmaceutically acceptablecarrier” as used herein is intended to include diluents such as salineand aqueous buffer solutions. It may be necessary to coat the compoundwith, or co-administer the compound with, a material to prevent itsinactivation. The active agent may also be administered parenterally, orintraperitoneally. Dispersions can also be prepared in glycerol, liquidpolyethylene glycols, and mixtures thereof and in oils. Under ordinaryconditions of storage and use, these preparations may contain apreservative to prevent the growth of microorganisms or otherstabilizing formulation (e.g. FTA).

Pharmaceutical compositions suitable for injectable use may beadministered by means known in the art. For example, sterile aqueoussolutions (where water soluble) or dispersions and sterile powders forthe extemporaneous preparation of sterile injectable solutions ordispersion may be used. In all cases, the composition can be sterile andcan be fluid to the extent that easy syringability exists. It might bestable under the conditions of manufacture and storage and may bepreserved against the contaminating action of microorganisms such asbacteria and fungi. The pharmaceutically acceptable carrier can be asolvent or dispersion medium containing, for example, water, ethanol,polyol (for example, glycerol, propylene glycol, and liquidpolyetheylene glycol, and the like), and suitable mixtures thereof. Theproper fluidity can be maintained, for example, by the use of a coatingsuch as lecithin, by the maintenance of the required particle size inthe case of dispersion and by the use of surfactants. Prevention ofmicroorganisms can be achieved by heating, exposing the agent todetergent, irradiation or adding various antibacterial or antifungalagents.

Sterile injectable solutions can be prepared by incorporating activecompound (e.g. a compound that induces an immune response to one or moredengue virus serotypes) in the required amount in an appropriate solventwith one or a combination of ingredients enumerated above, as required,followed by filtered sterilization.

Upon formulation, solutions will be administered in a manner compatiblewith the dosage formulation and in such amount as is therapeuticallyeffective. The formulations are easily administered in a variety ofdosage forms, such as the type of injectable solutions described above.It is contemplated that compositions are especially suitable forintramuscular, subcutaneous, intradermal, intranasal and intraperitonealadministration. A particular ratio may be sought such as a 1:1, 1:2 orother ratio (e.g. PFUs of a given dengue virus serotype)

The active therapeutic agents may be formulated within a mixturepredetermined ratios. Single dose or multiple doses can also beadministered on an appropriate schedule for a given situation (e.g.prior to travel, outbreak of dengue fever).

In another embodiment, nasal solutions or sprays, aerosols or inhalantsmay be used to deliver the compound of interest. Additional formulationsthat are suitable for other modes of administration includesuppositories and pessaries.

Certain formulations can include excipients, for example, pharmaceuticalgrades of mannitol, lactose, starch, magnesium stearate, sodiumsaccharine, cellulose, magnesium carbonate and the like.

A pharmaceutical composition may be prepared with carriers that protectactive ingredients against rapid elimination from the body, such astime-release formulations or coatings. Such carriers include controlledrelease formulations, such as, but not limited to, microencapsulateddelivery systems, and biodegradable, biocompatible polymers, such asethylene vinyl acetate, polyanhydrides, polyglycolic acid,polyorthoesters, polylactic acid and others are known.

Pharmaceutical compositions are administered in an amount, and with afrequency, that is effective to inhibit or alleviate side effects of atransplant and/or to reduce or prevent rejection. The precise dosage andduration of treatment may be determined empirically using known testingprotocols or by testing the compositions in model systems known in theart and extrapolating therefrom. Dosages may also vary with the severityof the condition. A pharmaceutical composition is generally formulatedand administered to exert a therapeutically useful effect whileminimizing undesirable side effects. In general, dose ranges from about10² to 10⁶ PFU can be administered initially and optionally, followed bya second administration within 30 days or up to 180 days later, asneeded. In certain embodiments, a subject can receive dualadministration of a mono, bi-, tri or tetravalent composition disclosedherein wherein the composition is a single composition mixture or haspredetermined compositions of different dengue virus serotypes. In someembodiments, a DEN2/4 chimera can be present in higher concentrationsthan other dengue virus serotypes such as a live, attenuated dengue-1.

It will be apparent that, for any particular subject, specific dosageregimens may be adjusted over time according to the individual need.

In one embodiment, a composition disclosed herein can be administered toa subject subcutaneously or intradermally.

The pharmaceutical compositions containing live, attenuated dengueviruses may be administered to individuals, particularly humans, forexample by subcutaneously, intramuscularly, intranasally, orally,topically, transdermally, parenterally, gastrointestinally,transbronchially and transalveolarly. Topical administration isaccomplished via a topically applied cream, gel, rinse, etc. containingtherapeutically effective amounts of inhibitors of serine proteases.Transdermal administration is accomplished by application of a cream,rinse, gel, etc. capable of allowing the inhibitors of serine proteasesto penetrate the skin and enter the blood stream. In addition, osmoticpumps may be used for administration. The necessary dosage will varywith the particular condition being treated, method of administrationand rate of clearance of the molecule from the body.

In certain embodiments of the methods of the present invention, thesubject may be a mammal such as a human or a veterinary and/or adomesticated animal or livestock or wild animal.

Therapeutic Methods

In one embodiment of the present invention, methods provide for inducingan immune response to dengue virus serotype(s) using a mono, bi-, tri ortetravalent formulation of live, attenuated and/or chimeric viralconstructs contemplated herein.

Embodiments of the present invention is further illustrated by thefollowing non-limiting examples, which are not to be construed in anyway as imposing limitations upon the scope thereof. On the contrary, itis to be clearly understood that resort may be had to various otherembodiments, modifications, and equivalents thereof which, after readingthe description herein, may suggest themselves to those skilled in theart without departing from the spirit of the present invention or thescope of the appended claims.

EXAMPLES

The following examples are included to demonstrate certain embodimentspresented herein. It should be appreciated by those of skill in the artthat the techniques disclosed in the Examples which follow representtechniques discovered to function well in the practices disclosedherein, and thus can be considered to constitute preferred modes for itspractice. However, those of skill in the art should, in light of thepresent disclosure, appreciate that many changes can be made inparticular embodiments which are disclosed and still obtain a like orsimilar result without departing from the spirit and scope herein.

Example 1

In some exemplary methods, compositions used to generate as referred toherein as “master virus seeds (MVS)” are disclosed. These compositionsmay be derived from one or more live, attenuated dengue viruses, such asDEN-1, DEN-2, DEN-3, and DEN-4. In certain methods, compositions may bederived from one or more live attenuated Dengue viruses that include butare not limited to, specific constructs disclosed herein referred to asDENVax-1, DENVax-2, DENVax-3, and DENVax-4. In other exemplary methods,strategies used to generate and characterize these compositions areprovided. In yet other embodiments, tetravalent dengue virusformulations and genetic and phenotypic characterization of theseformulations are provided.

Production and Analysis of Pre-master DENVax Viruses

Certain procedures were performed to generate pre-master dengue virusseeds, such as serial amplification and purification of dengue viruses(e.g. DENVax). First, DENVax viruses were re-derived by transfection ofviral RNA transcribed from the full-length recombinant DENVax cDNA intoproduction-certified cells (e.g. Vero cells), resulting in P1(passage 1) virus seed. The four P1 viruses from each of dengue-1 todengue-4 were then amplified and plaque purified to obtain the candidatepre-master vaccine P7 seeds (see Table 1). Certain tests were performedto analyze passages of dengue viruses. For example, full-length genomesequencing demonstrated that all four of the P2 (passage 2) seed viruseswere genetically identical to their homologous progenitor,research-derived, research-grade candidate vaccine virus. The originalplaque phenotypes were also retained in the P2 viruses. Six plaquepurified viruses (P3 A-F) were isolated for each serotype of denguevirus (e.g. DENVax1-4) from the P2 seeds, and each isolated plaque wasdirectly plaque purified two more times. The third plaque purification(P5) of each virus was amplified twice (P6 A-F and P7 A-F) in Vero cellsto produce the potential pre-master P7 DENVax seeds (Table 1).

TABLE 1 Example of a cGMP Rederivation of DENVax Viruses in WCB-VeroCells Passage Seed Production/Purification Characterizations P1Transfect WCB-Vero with Plaque titrate transcribed viral RNAs P2 AmplifyP1 virus Full genome sequence P3 Pick 6 plaques (A-F)/serotype Plaquefrom P2 plaque assay purification P4 Pick plaques A-F from P3 plaquePlaque assay purification P5 Pick plaques A-F from P4 plaque Plaqueassay purification P6 Amplify P5 A-F plaques Plaque titrate P7Pre-master seeds: Amplify P6 A-F Full genome sequence, TaqMAMA, Plaquephenotypes P8* MVS: Amplify selected P7 virus seed Full genetic andphenotypic characterization P9 WVS: Amplify P8 Master Seed viruses Fullgenome sequence, TaqMAMA P10 BVS: Amplify P9 Working Seed viruses Fullgenome sequence, TaqMAMA *One optimal P7 seed (A, B, C, D, E, or F) wasselected based on the genetic and plaque analysis to make P8 MVS

Some tests were further performed to characterize P7 DENVax seeds, suchas analysis of genome sequences and plaque phenotypes of the P7 seeds,and comparison with P2 seeds (Table 2). Plaque phenotypes of the P7viruses were generally similar to those of the P2 seeds. In someexemplary experiments, virus titers were monitored. Virus titers reachedover 6.0 log pfu/ml for most of the P7 seeds, except for 5 viruses.Genome sequencing of more than 60 candidate vaccine virus seeds after 10or more serial passages in Vero cells identified no reversion event atNS1-53 and NS3-250 of the three major attenuation determinants of theDENV-2 PDK-53 genetic vector, suggesting that these 2 loci are quitestable in candidate vaccine virus seeds. All sequence chromatograms ofthe 24 candidate strains generated from both forward and reversesequencing for these two sites were homogenous without any minornucleotide populations evident at the NS1-53 and NS3-250 genetic loci.In contrast to the NS1 and NS3 sites, different levels of reversions atthe 5′NCR-57 attenuation locus were identified from multiple seriallypassaged research grade vaccine viruses, suggesting this locus might notbe as stable as NS1 and NS3 after multiple passages in cell culture.Therefore, a sensitive mismatch amplification assay (TaqMAMA) wasdeveloped to accurately measure the reversion rate at the 5′NCR-57 locusby real-time RT-PCR. In some studies, the 5′NCR-57 reversion rates ofall 24 of the P7 seeds were measured by the TaqMAMA. Depending on theconcentration of the input viral RNA for each virus in the assay, thesensitivity limit of the TaqMAMA ranged between 0.01% and 0.07%reversion, which is much more sensitive than the 10-30% reversionsensitivity limit detectable by consensus genome sequence analysis. Theresulting data illustrates that 15 of the 24 P7 viruses had minimal orundetectable reversion (<0.07%), one virus (DENVax-3-D) had almost 100%reversion, and 8 viruses (1 DENVax-1, 1 DENVax-2, 2 DENVax-3, and 4DENVax-4) had partial reversion ranging from 0.08% to 12.85% (Table 2).Full-length genome sequencing was conducted for 16 of the 24 P7 viruseswith low levels of 5′NCR57 reversion as measured by TaqMAMA. All thesequenced viruses maintained the other two DENVax attenuationdeterminants (NS1-53, NS3-250), and all had acquired additionalmutations that were not present in the original, engineered recombinantcDNA clones (Table 2). In one exemplary target vaccine composition,DENVax-1-A, DENVax-2-F, DENVax-3-F, and DENVax-4-F were selected astarget pre-master seed for each serotype because their genotypes andplaque phenotypes most closely resembled those of the originallydesigned vaccine recombinants. The DENVax-1-A, DENVax-2-F, andDENVax-4-F had two non-synonymous mutations, and the DENVax-3-F had one.The evidence suggests these additional mutations observed in these 4pre-master seeds do not cause safety concerns or immunogenicityalterations for the viruses. These pre-master seeds were furtheramplified to generate the MVS (master seed, designated as P7, Table 1).

Exemplary methods provided herein used purified in-vitro transcribedviral RNA from cloned cDNA plasmid as the pure source to transfectvaccine-certified Vero cells to generate vaccine virus. Serial plaquepurifications and full-genome sequence analyses were incorporated intothe manufacturing procedures to ensure manufactured vaccine seeds withoptimal purity and genetic stability. Six cloned viruses were preparedas potential pre-master seeds for each serotype of DENVax. Throughgenomic analysis, including TaqMAMA and complete genomic sequencing, aswell as characterization of viral plaque phenotypes, pre-master seedswere chosen to advance to master virus seeds production for eachserotype (serotypes 1-4). The selected pre-master seeds had undetectablereversions (<0.01% or <0.07%) at the 5′NCR-57 locus, with 1 or 2 aminoacid substitutions in their genomes, and retained the small plaquephenotypes previously observed.

TABLE 2 Characterizations of pre-master (P7) seeds Log₁₀ Virus Clone^(a)TaqMAMA^(b) pfu/ml Plaque^(c) Mutations identified in genome^(d)DENVax-1 A ** 6.85 P2 NS2A-116 I-L, NS2B-92 E-D, one silent B * 6.93 P2nd^(e) C * 6.93 D nd D ** 7.02 D C-67 K-A; one silent E 0.57% 7.28 P2 ndF ** 7.18 P2 E473 T-M; one silent DENVax-2 A 0.03% 6.33 P2 NS1-341 K-NB * 6.33 P2 E-305 K-T, two silent C * 5.84 L NS4A-18 T-A, four silent D0.08% 6.20 P2 NS2B-99 I-L, one 3′NCR E 0.03% 6.31 P2 prM-52 K-E, NS5-412I-V, two silent F ** 6.15 P2 prM-52 K-E, NS5-412 I-V DENVax-3 A * 6.00P2 NS5-200 K-N, one silent, one 3′NCR B 0.05% 6.27 P2 NS2A-33 I-T,NS2A-59 M-T C 0.30% 6.25 P2 nd D 100.00%  6.27 P2 nd E 0.31% 6.00 P2 ndF ** 6.30 P2 E-223 T-S, one silent DENVax-4 A 0.47% 5.60 P2 E323 K-R/K,NS2B-21 L-F/L, NS2B-39 T-S, one silent B * 5.65 D NS2A-126 A-V; NS4A-5N-D; NS5-383 K-R, one silent C 4.50% 5.90 P2 nd D 12.85%  5.97 D nd E0.52% 6.85 S prM-85 E-D, NS2B-45 T-A, NS5-320 M- T, NS5-551 E-G, twosilent F 0.02% 6.93 S NS2A-66 D-G, NS4A-21 A-V, four silent ^(a)Clonedviruses (by serial plaque purifications) selected for furtherdevelopment of MVS are designated bold. ^(b)* Reversion rate < 0.07%(detection limit). ** Reversion rate < 0.01% (detection limit)^(c)Plaque phenotypes: P2: similar to P2 virus; L = larger than P2virus, D = similar size, but appear somewhat different in clearness ofthe plaques; S = smaller than P2. ^(d)Substitutions differing from theengineered DENVax cDNA clones. Amino acid mutations are listed withresidue position of the virus protein and the changes (wt-mutation).Total number of silent mutations in structural and non-structural genesof each seed is listed. Mutations at non-coding region (NCR) are alsonoted. ^(e)nd = Not done. These clones had higher 5′NCR-57 reversionrates (by TaqMAMA) than other clones, so were excluded from furthersequence analysis.

Example 2

In some exemplary methods, compositions of master virus seeds, workingvirus seeds and bulk virus seeds as well as their genetic and phenotypiccharacterization are described. These compositions are provided formanufacture of clinical materials and ultimately commercial vaccinesupplies. Serial plaque purifications and full-genome sequence analyseswere incorporated into the manufacturing process to ensure compositionsof vaccine seeds with optimal safety and genetic stability formanufacture of clinical trial materials.

Production and Manufacturing Quality Controls for MVS, WVS, and BVS

In some studies, MVS of the 4 DENVax were produced by amplifying thepre-master P7 seed in certified Vero cells. In other studies, MVS wereused to make large amount of WVS in cell factories. Further, the BVSstocks of DENVax were amplified from the WVS and were formulated intotetravalent drug product mixtures to be used used for human clinictrials. Quality controls for product release were performed in someexemplary methods, including, but not limited to, testing all of theMVS, WVS, and BVS for identity, infectious titer, sterility, mycoplasma,and in vitro and in vivo adventitious agents. All seeds passed the virusidentity test using serotype-specific RT-PCR assays, which showedpositive amplification corresponding to its serotype and negative forheterologous serotypes (data not shown). No detectable mycoplasma oradventitious agents were detected in the MVS, WVS, or BVS stocks.

Genetic Analysis of the MVS, WVS, and BVS

In certain exemplary methods, after generation of MVS from the selectedpre-MVS (P7) strains selected above were produced and the respectiveviral RNA was sequenced again. Full-length genome sequencing revealedthat the MVS for DENVax-1 was identical to its pre-master seed, whilethe WVS and subsequent BVS acquired 2 additional substitutions at E-483and NS4B-108 (see Tables 2 and 3). The Ala substitution at E-483represented part of the genotype in the MVS, but became the dominantgenotype in BVS. DENVax-2 and DENVax-3 were identical to theirrespective pre-master seeds (Table 2 and 3). The DENVax-2 MVS wasidentical to its pre-master seed, and the WVS and BVS had 2 additionalmutations at NS4A-36 and NS4B-111. Both mutations were partial in WVSand were the major genotype in the BVS. The MVS of DENVax-3 was againidentical to the pre-master seed, but the WVS and BVS contained anadditional aa substitution at NS4A-23. The DENVax-4 MVS acquired anadditional amino acid mutation, at locus NS2A-99 (from Lys to Lys/Argmixed genotype) during production of the MVS (Table 3). Its WVS and BVSretained the NS2A-99 Lys/Arg mixed genotype, and the BVS had an extraNS4B-238 Ser/Phe mixed genotype. Consensus sequence results alsoconfirmed that MVS, WVS as well as BV retained the three geneticdeterminants of attenuation at the 5′NCR-57, NS1-53, and NS3-250 loci.Analysis of the least stable attenuating locus by TaqMAMA demonstratedthat the 5′NCR-57 reversion rate between <0.7% to and 0.13% among MVS,≤0.07% among WVS, and between <0.07 and 0.21% among BVS. A 3% reversionat the 5′NCR-57 locus was considered the maximum permissible rate foracceptance of a vaccine lot (Table 3).

TABLE 3 Nucleotide and amino acid substitutions in DENVax seeds DENVaxNucleotides Amino Acids Pre-master MVS^(a) WVS^(a) BVS^(a) DENVax-1 2384G-C E-483 Gly-Ala - - Gly/Ala Ala 3823 A-C NS2A-116 Ile-Leu Leu Leu LeuLeu 4407 A-T NS2B-92 Glu-Asp Asp Asp Asp Asp 7148 C-T NS4B-108Thr-Ile - - Ile Ile 7311 A-G silent G G G G TaqMAMA 5′NCR-57 reversion%^(b) -- - - - DENVax-2  592 A-G prM-52 Lys-Glu Glu Glu Glu Glu 6481 G-CNS4A-36 Ala-Pro - - Ala/Pro Pro 7156 C-T NS4B-111 Leu-Phe - - Leu/PhePhe 8803 A-G NS5-412 Ile-Val Val Val Val Val TaqMAMA 5′NCR-57 reversion%^(b) -- - 0.07% 0.21% DENVax-3 1603 A-T E-223 Thr-Ser Ser Ser Ser Ser6436 G-A NS4A-23 Asp-Asn - - Asn Asn 7620 A-G silent G G G G TaqMAMA5′NCR-57 reversion %^(b) -- - - - DENVax-4  225 A-T silent T T T T 3674A-G NS2A-66 Asp-Gly Gly Gly Gly Gly 3773 A-A/G NS2A-99 Lys-Lys/Arg -Lys/Arg Lys/Arg Lys/Arg 5391 C-T silent T T T T 6437 C-T NS4A-21 Ala-ValVal Val Val Val 7026 T-C silent T/C T/C T/C T/C 7538 C-C/T NS4B-238Ser-Ser/Phe - - Ser/Phe Ser/Phe 9750 A-C silent C C C C TaqMAMA 5′NCR-57reversion %^(b) - 0.13% - - ^(a)Bold: Changes started at MVS stocks.^(b)“--” indicates reversion rate <0.01% (detection limit), “-”indicates reversion rate <0.07% (detection limit)

Full-genome sequence analysis revealed that an additional amino acidmutation developed in the DENVax-4 MVS, while the other three DENVax MVSlots retained the consensus genome sequence of their pre-master seeds.Overall, from deriving of the P1 seeds to the pre-master (P7) seeds,only 1 or 2 non-synonymous mutations occurred in a given seed. From P1to MVS (P8) seeds, 2 to 7 nucleotide substitutions were identified inany given DENVax seed and only 2 to 3 of these substitutions resulted inamino acid changes. Thus, minor changes occurred. RNA viruses areerror-prone in their genome replication, so genetic substitutions inflavivirus genome during cell passages are not unexpected. None of thesilent mutations in the MVS were within the 5′ or 3′NCR that may affectvirus replication. Only the change in prM-52 Lys-Glu of the DENVax-2,and the substitution in NS2A-66 Asp-Gly of DENVax-4 are not conservativechanges. The NS2A-66 mutation of the DENVax-4 is in the nonstructuralbackbone part of the DENV-2 PDK-53. Although NS2A-66 locus is usuallyAsp among various strains of DENV-2, it is usually Gly for DENV-4. It ispossible that the Asp to Gly change in the DENVax-4 is relevant forfitness of the DENVax-4 in Vero cells. The DENVax-2 prM-52 mutationresides in the C-terminal portion of the prM that is cleaved out fromthe mature virus particles. In some exemplary methods, phenotypiccharacterization was performed to confirm that none of the mutations inthe MVS seeds significantly altered the attenuation phenotypes of thevaccine.

The DENVax viruses demonstrated high genetic stability during themanufacturing process. The three defined DENV-2 PDK-53 attenuation locilocated in 5′NCR, NS1-53, and NS3-250 remained stable in the consensusgenome sequence upon serial passage of the DENVax from pre-Masterstrains to bulk vaccine preparations. The highly sensitive TaqMAMA ofthe 5′NCR-57 locus demonstrated minimal or undetectable reversion in theMVS, WVS (P9/Working), and BVS (Bulk Virus Seed for vaccines) of denguevirus serotypes. The 5′NCR-57 reversion rates of the DENVax BVSpreparations (P10-equivalent) were significantly lower than the 5′NCR-57reversion rates that evolved in research-grade vaccine candidates after10-serial passages in Vero cells (4-74% reversion). The strategy forlarge-scale manufacturing of the DENVax seeds provided herein resultedin a genetically stable vaccine seed which retained the attenuationmarkers in the candidate vaccine viruses.

Plaque Phenotype of DENVax MVS

In one exemplary method, plaque phenotypes of the DENVax MVS werecompared with wild type Dengue viruses and their homologousresearch-grade chimeric viruses in Vero cells (FIG. 2). All of the MVSof DENVax-1, -2, and -3 produced plaques that were significantly smallerthan their wild type homologs and very similar (within 0.4-mmdifferences) to their homologous research-grade viruses in Vero cells.DENVax-4 MVS was also significantly smaller than the wild type DENV-4,but was slightly larger (0.9 mm difference) than the original labderived D2/4-V chimera.

FIG. 2 represents an exemplary histogram illustrating plaque sizes ofthe DENVax MVS in contrast with control wild type viruses andresearch-grade vaccine candidate viruses. Mean plaque diameters (mm)±SD(error bars) of the virus plaques in Vero cells under agarose overlaymeasured on day 9 pi. The wild type DEN viruses, represented by blackbars, and previously published research-grade vaccine candidate viruses,represented by white bars, were included for control and comparison tothe DENVax master vaccine seeds represented by grey bars.

Temperature Sensitivity of DENVax MVS

In another exemplary method, temperature sensitivity was tested in Verocells for the DENVax MVS and compared with their homologous wild typeand the original research-grade chimeric vaccine virus. The wild type(wt) DENV-3 16562 was not temperature sensitive. The wt dengue virusserotype 1 and dengue virus serotype-4 were moderately temperaturesensitive at 39° C. (titers were approximately 1.0 log₁₀ pfu/ml lower at39° C. than at 37° C., FIG. 3). Wt Dengue virus serotype-2 16681 was themost temperature sensitive of the wt Dengue viruses tested, and resultedin a 100-fold titer drop at 39° C. DENVax-1, -2, and -3 were astemperature sensitive as their original homologous research-gradechimeric vaccine viruses (FIG. 2). Titers at 39° C. dropped between 2.0and 3.0 log₁₀ pfu/ml for these DENVax strains. DENVax-4 also wastemperature sensitive, demonstrating a 5-fold reduction in titer.However, the original research-grade D2/4-V demonstrated about a 10-foldreduction in titer. The final stabilized DENVax-4 MVS contained F127(and other agents known to stabilize these formulations (FTA)), whichwas shown to enhance thermal stability of the Dengue viruses. Thepresence of the F127 in DENVax-4 MVS likely contributed to the lesspronounced temperature sensitivity of the virus in the Vero cultureassay. In a separate experiment, temperature sensitivity of anMSV-derived DENVax-4 strain in the absence of F127 was furtherevaluated. To remove the F127 from the strain, viral RNA was isolatedfrom a DENVax-4 bulk virus preparation and was transfected into Verocells. This DENVax-4 virus appeared to be as temperature sensitive asthe D2/4 V research strain (titer reduced 1.5 log₁₀ pfu/ml) on day 3 piin the absence of F127 (FIG. 3).

FIG. 3 illustrates an exemplary histogram illustrating temperaturesensitivities of DENVax MVS. The wild type Dengue viruses and previouslypublished research-grade vaccine candidate viruses were included forcomparison. The DENVax-4 MVS contains additional F-127 that can mask thetemperature sensitivity results of the virus in this assay. A separateexperiment analyzing a surrogate DENVax-4 in the absence of F127 wasalso included. Mean titers±SD (error bars) of the viruses replicated inVero cells at 37° C. or 39° C.

DENVax MVS Replication in Mosquito C6/36 Cells

In some exemplary methods, the DENVax MVS were grown in C6/36 cells toverify their retention of the in vitro attenuation phenotype, with theknowledge that the research-grade chimeric vaccine viruses retained theattenuation phenotype of the backbone DENV-2 PDK53 virus in thesemosquito cells. Compared to the wt Dengue viruses, DENVax-1, DENVax-2and DENVax-4 MVS showed significant growth reduction (at least 3 log₁₀pfu/ml reduction) in C6/36 cells on day 6 pi (FIG. 4). The DENVax-3 MSValso exhibited reduced growth compared to the wt DENV-3 16562, but thereduction was not as marked (1-2 log₁₀ pfu/ml reduction). However, theC6/36 titers of the DENVax-3 seed lots were similar (within 1 log₁₀pfu/ml difference) to the C6/36 titer of the original research-gradechimeric D2/3-V vaccine virus.

FIG. 4 illustrates an exemplary histogram plotting restricted growth ofDENVax MVS (grey bars) in C6/36 cells in comparison with wt Dengueviruses (black bars) and research-grade vaccine viruses (white bars).Mean titers±SD (error bars) of the viruses replicated in C6/36 cells 6days pi.

Virus Infection, Dissemination, and Transmission Rates in WholeMosquitoes

In some exemplary methods, the infection and dissemination rates of theDENVax were compared with their parental wt Dengue viruses. In certainexemplary experiments, oral infection experiments were conducted in Ae.aegypti mosquitoes. Infectious blood meals were back-titrated to measurethe virus titers and only the experiments with similar virus titers inthe blood meal (less than 1 log₁₀ pfu/ml differences) between parentalDengue viruses and DENVax for each serotype were included forcomparisons in Table 4. DENVax-1, DENVax-2, and research-grade D2PDK-53-VV45R did not infect mosquitoes through oral feeding, which issignificantly different (p<0.0001) from their parental viruses, DENV-116007 (44% infection) and DENV-2 16681 (43.3% infection). Because nomosquito was infected by DENVax-1 and -2, there was little to nodissemination concern for these two vaccine viruses. While DENVax-4 didinfect some mosquitoes through oral feeding (2 out of 55), the infectionrate was significantly lower (p<0.05) than its parental wt virus, DENV-41036 (8 out of 50). DENVax-3 did not infect any mosquitoes in twoexperiments with blood meal viral titers of 5.2±0.02 log₁₀ pfu/ml (Table4), and in a separate experiment with blood meal viral titer of 6.0log₁₀ pfu/ml, only 1 out of 30 mosquitoes became infected (data notshown). However, wt Dengue virus-3 16562 also had a very low infectionrate (8%) at 5.2 log₁₀ pfu/ml, and the rate did not increase in aseparate experiment with a higher blood meal viral titer at 6.2 log₁₀pfu/ml (3%, 1 positive out of 30 mosquitoes, data not shown). Althoughthe wild type (wt) Dengue virus-3 and Dengue virus-4 had significantlylower infection rates than the wt Dengue virus-1 and Dengue virus-2, themean virus titers in the infected mosquitoes were similar (3.1 to 3.9log₁₀ pfu/mosquito). In contrast, the DENVax-4 titers from the twoinfected mosquitoes were both minimal (0.7 log₁₀ pfu/mosquito), whichwas 1,000-fold lower than the titer from the mosquitoes infected by wtDengue virus serotype-4 1036 (3.9±1.5 pfu/mosquito).

For those mosquitoes that were infected, dissemination out of the midgutcould be assessed by determining whether virus was present in the legs.The four parental DENVs resulted in dissemination rates ranging between36.3% and 62.5%, and their mean virus titers (in log₁₀ pfu) from thelegs were between 0.9±0.3 and 2.2±0.7 (excluding negative samples).Neither of the two DENVax-4 infected mosquitoes resulted in virusdissemination to the legs (Table 4). While disseminated virus wasdetectable in the legs, none of the four wt Dengue viruses wasdetectable in saliva of orally infected mosquitoes, suggesting that oralfeeding conditions may not be sufficiently sensitive to measure thetransmission rate of these DENVs. Therefore, in other exemplary methods,highly stringent artificial mosquito infections by direct IT inoculationwere subsequently performed (Table 4). Except for DENVax-4, all viruses(wt and DENVax) achieved 100% infection of the IT inoculated Ae.aegypti. The DENVax-4 inoculum had a slightly lower viral titer than theother three viral inocula, but it still successfully infected 70% of theinoculated mosquitoes. Despite the high body infection rates achieved byIT inoculation, all four DENVax viruses exhibited significantly lower(p<0.005) or non-detectable transmission rates (0-10%) compared to thewt Dengue viruses (43-87%, Table 4). The DENVax viruses demonstratedlittle to no infection and dissemination after oral feeding, and thehighly stringent IT results affirmed the minimal transmission capacityof these DENVax viruses in Ae. aegypti.

TABLE 4 Virus infection, dissemination, and transmission rates in wholemosquitoes Oral Feed IT inoculation Blood Body Body Meal^(a) Titer^(c)Titer^(c) Saliva^(f) Mean ± Infection^(b) Mean ± Dissemination^(e)Inoculum Infection^(b) Mean ± % Virus SD % (P/N) SD p^(d) % (P/N)^(f)pfu/dose % (P/N) SD (P/N) p^(d) DENV-1 6.6 44.0%   3.6 ± 1.5 36.3% 53.9100% 4.7 ± 0.48 43% 16007 (11/25)  (4/11) (30/30) (13/30)  DENVax-1 6.90% NA <0.0010 NA 67.8 100% 3.4 ± 0.39 10% <0.005 (0/30) (30/30) (3/30)DENV-2 6.6 43.3%   3.1 ± 1.5 38.5% 67.8 100% 5.2 ± 0.34 87% 16681(13/30)  (5/13) (30/30) (26/30)  D2 PDK53- 6.4 0% NA <0.0001 NA 56.4100% 4.0 ± 0.20  0% <0.0001 VV45R (0/30) (30/30) (0/30) DENVax-2 6.4 0%NA <0.0001 NA 52.7 100% 3.5 ± 0.27  7% <0.0001 (0/30) (30/30) (2/30)DENV-3 5.2 8% 3.8 ± 0.2   50% 34.0 100% 4.2 ± 0.50 67% 16562 (2/25)(1/23) (30/30) (20/30)  DENVax-3  5.2 ± 0.02 0% NA 0.108 NA 37.3 100%3.3 ± 0.36  3% <0.0001 (0/50) (30/30) (1/30) DENV-4 5.8 ± 0.5 16%  3.9 ±1.5 62.5% 69.4 100% 5.2 ± 0.45 70% 1036 (8/50) (5/8)  (30/30) (21/30) DENVax-4 5.4 ± 0.4 3.6%   0.7 ± 0.0 0.033   0% 11.8  70% 1.1 ± 0.46  0%<0.0001 (2/55) (0/2)  (21/30) (0/21) ^(a)Virus titers or Mean ± standarddeviation if from more than 1 experiment in blood meal (log₁₀ pfu/ml) byback titration ^(b)Rate of virus detected in mosquito bodies. P/N =positive/total mosquitoes ^(c)Mean virus titers ± standard deviation(log₁₀ pfu/mosquito) in mosquito body, only positive sample are includedfor calculation ^(d)Statistic analysis of the differences between wtDENV and DENVax by Fisher Exact probability ^(e)Rate of virus detectedin legs of the positively infected mosquitoes ^(f)Rate of virus detectedin saliva of the positively infected mosquitoes. Used to measuretransmission efficiency

Vector competence is an important safety component for live-attenuatedflavivirus vaccine viruses. Previously, the research-grade DENV-2PDK-53-VV45R virus and wt derivatives were tested in Ae. aegypti, andfound that the NS1-53-Asp attenuating mutation was the dominantdeterminant for impaired mosquito replication. The other two majorattenuation loci of the DENV-2 PDK-53 vaccine, nucleotide 5′NCR-57-T andNS3-250-Val, also exhibited some inhibiting effect on replication inmosquitoes, thus providing additional, redundant restrictions formosquito vector competence. Some exemplary methods described herein wereused to test the mosquito oral and IT infection and replication for allfour DENVax strains. DENVax-1, -2, and -3 did not infect any Ae. aegyptimosquitoes through oral infection (Table 4). The DENVax-4 infected only3.6% of orally exposed mosquitoes, a level significantly lower than thatof the wt DENV-4 with a replicative mean titer in the mosquito bodieslower than that of wt DENV-4 infected mosquitoes. Surprisingly, DENVax-4was detected in the legs of the infected mosquitoes, suggesting thatDENVax-4 was not able to disseminate from the mosquito midgut followingoral infection. The infection rates for the DENVax-1, -2, and -4 wereall significantly less than their wt counterparts, but the differencewas not significant between DENVax-3 and wt DENV-3 16562 due to the verylow infection rates for both viruses. Compared to other wt strains ofDENV assessed in Ae. aegypti collected from the same Mae Sot Province,Thailand, the parental wt Dengue virus strains used for engineeringDENVax appeared to have lower infectious and dissemination rates by oralinfection. The wt DENV-1 PU0359, DENV-2 PUO218, DENV-3 PaH881/88, andDENV-4 1288 used for engineering the Yellow Fever (YF) 17D vaccine-basedChimeriVax-DEN vaccines had infection rates ranging 47-77%. In contrast,the YF 17D vaccine cannot infect Ae. aegypti. Although the ChimeriVaxstrains contained the prM-E from these highly infectious wt DENV, theChimeriVax retain the mosquito attenuation phenotype of their YF 17Dreplicative backbone. Results provided herein also indicated that themosquito attenuation of DENV-2 PDK-53 backbone was maintained in theDENVax strains. In addition, using the wt Dengue virus strains withlower mosquito-infectivity in constructs included in compositionsdescribed herein provides an additional safety feature.

The oral infection results illustrate that the DENVax had minimummosquito infectivity and dissemination capacity. In addition, the moresensitive and stringent IT infection experiments were performed tofurther analyze the potential of DENVax to be transmitted by Ae.aegypti. The IT results demonstrated that all four DENVax viruses hadnon-detectable or minimal mosquito transmission potential compared totheir wt counterparts. DENVax transmission could only theoreticallyoccur if (1) vector feeds on a vaccinee with a sufficient viremia titerto infect mosquito midgut, (2) the virus is capable of replicating inthe midgut epithelium and able to subsequently disseminate out of themidgut, and (3) the disseminated virus can replicate in salivary glandand expectorate sufficient virus in saliva for transmission. Thethreshold of human viremia required to infect mosquitoes has not beenestablished adequately, but human viremia can be 10⁶-10⁸ mosquitoinfectious dose₅₀ (MID₅₀)/ml after natural wt DENV infection. This MID₅₀was based on direct IT inoculation of mosquitoes with diluted humanplasma. Analysis of DENVax in nonhuman primates indicated that viremiatiters following DENVax immunization were very low (less than 2.4 log₁₀pfu/ml) and lasted for 2-7 days. Given the low viremia levels and thelow mosquito infection, dissemination, and transmission capacity ofDENVax, it is unlikely that these vaccine viruses could be transmittedby mosquitoes in nature or cause viremia.

Therefore, it is proposed that any of the passages of any of theserotypes (P1-P10) could be used in a composition to generate a safe andeffective vaccine against one, two, three or all four dengue virusserotypes.

Neurovirulence in Suckling Mice

The original research-grade vaccine viruses were highly attenuated forneurovirulence in newborn ICR mice maintained in-house at DVBD/CDC. Allof these mice survived ic (intracerebral) challenge with 10⁴ pfu of eachvaccine virus. The wt Dengue virus serotype-2 16681 virus, on the otherhand, resulted in 62.5%-100% mortality in these CDC-ICR mice in variousexperiments. In some experiments, commercial ICR mice obtained fromTaconic Labs (Taconic-ICR) were used to study neurovirulence in newbornmice. It was observed that newborn Taconic-ICR mice were significantlymore susceptible to Dengue virus serotype-2 infection than the previousCDC-ICR mice. FIG. 5A summarizes the neurovirulence of wt Dengue virusserotype-2 16681 in CDC-ICR colony and Taconic-ICR newborn micechallenged ic with 10⁴ pfu of the virus. The Taconic-ICR mice (100%mortality in 32 mice, average survival time of 8.3±0.5 days) were moresusceptible to ic Dengue virus serotype-2 16681 challenge than theprevious CDC-ICR mice (91% fatalities in 72 mice, average survival timeof 14.6±2.3 days).

In other exemplary methods, in order to evaluate neurovirulence of theDENVax MVS, the Taconic-ICR mice initially were challenged ic(intracerebrally) with a dose of approximately 10⁴ pfu of wt Denguevirus serotype-2 16681, D2 PDK-53 VV45R, D2/3-V, or DENVax 1-4 virus inone (n=16) or two (n=31-32) experiments (FIG. 5B). At this dose, D2/3-Vresearch grade virus, as well as DENVax-1, and DENVax-3 MVS exhibitedfully attenuated neurovirulence phenotypes (no illness or mortality). Asexpected, wt Dengue virus serotype-2 was found to be “fatal”, withaverage mouse survival time (AST) of 8.3±0.8 days. In these Dengue virusserotype-2-sensitive Taconic-ICR mice, the D2 PDK-53-VV45R researchgrade virus resulted in 81.3% mortality. The DENVax-2 MVS and DENVax-4MVS were uniformly fatal in the Taconic-ICR, showing AST values of9.8±1.7, 10.2±1.4, and 11.3±0.4 days, respectively.

In some exemplary methods, the neurovirulence of wt Dengue virusserotype-2 16681 virus was compared with that of D2 PDK-53 VV45R,DENVax-2 MVS and DENVax-4 MVS, as well as D2/4-V research grade virus,at a 10-fold lower dose (10³ pfu, FIG. 5C). The wt Dengue virusserotype-2 retained a uniformly fatal neurovirulent phenotype, with ASTof 9.0±1.4 days, at this lower challenge dose. The other 4 virusesexhibited intermediate neurovirulence phenotypes, and the degree ofneurovirulence was serotype-specific. The D2 PDK-53-VV45R virus and itsDENVax-2 MVS cognate showed significant attenuation (32.3% survival withAST of 13.1±3.8 days and 31.2% survival with AST of 10.5±3.4 days,respectively). Both the DENVax-4 MVS and the research grade D2/4-V viruswere highly attenuated for neurovirulence (81.3% survival with AST of18.8±5.8 days and 100% survival, respectively). The results suggestedthat MVS of DENVax-1 and -3 exhibited complete attenuation ofneurovirulence, while DENVax-2 and -4 MVS lots retained attenuationphenotypes that closely resembled their homologous research-grade virusvaccine candidates.

FIGS. 5A-5C represent exemplary graphs illustrating neurovirulence innewborn mice tested with various compositions including wt Dengue virusserotype-2 and different attenuated Dengue viruses. Pooled results ofnumerous experiments summarizing the neurovirulence of wt Dengue virusserotype-2 16681 virus in CDC-ICR (n=72) and Taconic-ICR (n=32) newbornmice challenged ic with 10⁴ pfu of the virus (A). Neurovirulence ofDENVax MVS tested in Taconic-ICR mice with a dose of 10⁴ pfu (B) or 10³pfu (C). The numbers of animals tested per group in one experiment(n=16) or two pooled experiments (n=31 or 32) are indicated.

Plaque Phenotype of WVS, and BVS

Certain studies were performed to compare plaque phenotypes of WVS andBVS with MVS, wt Dengue viruses and their homologous lab derived,research-grade chimeras in Vero cells (FIG. 6). Mean plaque sizes werecalculated from 10 plaques for each vaccine virus, but from reducednumbers of wt DENV-1, -3, and -4. All of the MVS viruses of DENVax-1,-2, and -3 produced plaques that were significantly smaller than theirwt homologs and very similar (within 0.4-mm differences) to theirhomologous research-grade viruses in Vero cells. DENVax-4 MVS was alsosignificantly smaller than the wt DENV-4, but was slightly (0.9 mm)larger than the original lab derived D2/4-V chimera. With the exceptionof the DENVax-2, all of the WVS and BVS of the DENVax-1, -3, -4 retainedsignificantly smaller plaque sizes than those produced from their wthomologs. The DENVax-2 WVS and BVS produced plaques that were similar tothe plaques of wt DENV-2 virus in Vero cells, but when tested in LLC-MK₂cells all of the DENVax-2 manufactured seeds produced plaques that weresomewhat smaller than those of the wt DENV-2 (1.4±0.4) and similar tothe lab derived D2 PDK-53-VV45R (1.0±0.3) (FIG. 6).

Evaluation of the phenotypic markers of viral attenuation, includingsmall plaque phenotype, temperature sensitivity, reduced replication inmosquito cells, reduced infection/dissemination/transmission bymosquitoes, and reduced neurovirulence in newborn ICR mice, wereassessed for the compositions of MVS stocks. Results indicated that allof the DENVax retained the expected attenuation phenotypes similar tothe original research-grade vaccine viruses. Given the mutationsresponsible for attenuation are conserved in all MVS, WVS and BV, it canbe expected the attenuated phenotypes to be retained in the materialmanufactured for human clinical testing.

FIG. 6 represents an exemplary histogram illustrating plaque size of theDENVax MVS, WVS, and BVS. Mean plaque diameters±SD (error bars) of thevirus plaques in Vero or LLC-MK₂ cells under agarose overlay measured onday 9 pi. The wt DENVs and previously published research-grade vaccinecandidate viruses were included for control and comparison.

Virus Replication in Mosquito C6/36 Cells

Previous studies demonstrated that the research-grade PDK-53-basedchimeric vaccine viruses retained the attenuation phenotype of thebackbone DENV-2 PDK53 virus in C6/36 cells. In some exemplary methods,the DENVax MSV, WVS, and BVS were grown in C6/36 cells to verify theirretention of this in vitro attenuation marker after large scalemanufacturing. Compared to the wt Dengue viruses, except for DENVax-3,the manufactured seeds showed marked growth reduction (at least 3 log₁₀PFU/ml reduction) in C6/36 cells on day 6 pi (FIG. 7). The DENVax-3seeds also exhibited reduced growth compared to the wt DENV-3 16562, butthe reduction was not as marked (1-2 log₁₀ PFU/ml reduction). However,the titers of the DENVax-3 seed lots were similar (within 1 log₁₀ PFU/mldifference) to the original research-grade chimeric D2/3-V vaccinevirus.

FIG. 8 represents an exemplary histogram plotting restricted growth ofDENVax MVS, WVS, and BVS in C6/36 cells. Mean titers±SD (error bars) ofthe viruses replicated in C6/36 cells 7 days pi. The wt Dengue virusesand previously published research-grade vaccine candidate viruses wereincluded for comparison.

Neurovirulence in Suckling Mice

Additional experiments were performed to analyze neurovirulence innewborn ICR mice. At an intracranial dose of 10⁴ PFU, the survival ratesfor wt DENV-2 16681 and the D2 PDK-53-VV45R were 0% and 18.8%,respectively (FIG. 9A) in the ICR mice, but were about 20% for wt DENV-216681 and 100% for the D2 PDK-53-VV45R in the CDC ICR mice. In thisstudy, DENVax-1 and DENVax-3 MVS were attenuated (100% survival) for themice at a dose of 10⁴ PFU, but the MVS of DENVax-2 and DENVax-4 caused100% mortality at the dose of over 10⁴ PFU (FIG. 5A). However, whentested at a dose of 10³ PFU of virus, the DENVax-2 (31.3% survival) andDENVax-4 (81.3% survival) showed reduced neurovirulence relative to wtDengue virus serotype-2 16681 (0% survival), and their survival rateswere similar to those of the research-grade vaccine candidates D2PKD-53-VV45R (32.3%) and D2/4-V (100%), respectively (FIG. 9B).Although, wt DENV-1, -3, or -4 were not included for comparison in thisstudy, previous work demonstrated that wt DENV-1 16007 was attenuated inthe CDC-ICR mice by the is route, while both wt DENV-3 16562 and DENV-41036 were highly virulent (0% survival) for the CDC-ICR mice. It islikely that these 3 wt DENV would exhibit similar or greater virulencein the more susceptible Taconic ICR mice. Therefore, inclusion of thesewt Dengue viruses for comparison with their homologous DENVax MVSs wasconsidered to be uninformative. This study indicated that all 4 DENVaxMVSs and original laboratory derived candidate vaccine viruses exhibitcomparable mouse attenuation phenotypes relative to the wt DENV-2 16681.

FIGS. 9A-9B represent exemplary graphs of data of neurovirulence ofDENVax MVS in newborn ICR mice. (A) IC inoculations of the virus at doseof 10⁴ PFU. (B) IC inoculation of the virus at dose of 10³ PFU

All seed lots of the DENVax were tested for the identity, sterility, andfreedom from undesirable agents. Full-genome sequence analysis revealedthat one extra amino acid mutation evolved in the DENVax-4 MVS, whilethe other 3 DENVax MVSs retained the consensus genome sequence of theirpre-master seeds. In WVS lots, the DENVax-3 acquired an extra amino acidmutation and the other 3 serotypes accumulated 2 extra amino acidsubstitutions, relative to their pre-master seeds. Genome sequences ofall the 4 BVS lots were identical to their WVS lots. Overall from the P2seeds to the pre-master (P7) seeds, only 1 or 2 non-silent mutationsoccurred in a given seed. Between pre-master and BCS (P10) seeds, only 1to 2 nucleotide substitutions were observed, all of which occurred inNS2A, 4A, or 4B, with the exception of single nucleotide changeresulting in a conserved glycine and alanine at residue E-483. From P2to BVS (P10) seeds, total 3 to 8 nucleotide substitutions wereidentified in any given DENVax seed, and only 2 to 4 of thesesubstitutions resulted in amino acid changes. None of the silentmutations in the BVS were within the 5′- or 3′-NCR region which mayaffects virus replication. These results suggest that the DENVax viruseswere genetically highly stable during manufacture. The three definedDENV-2 PDK-53 attenuation loci located in 5′NCR, NS1-53, and NS3-250remained unchanged in the consensus genome sequence upon serial passageof the DENVax to generate BVS stocks. The highly sensitive TaqMAMA ofthe 5′-NCR-57 locus showed minimal or undetectable reversion in the MVS,WVS, and BVS of DENVax. The highest reversion rate of 0.21% wasidentified in the DENVax-2 BVS. The reversion rates of theP10-equivalent BVS (<0.07% to 0.21%) were significantly lower than thereversion rates that evolved in other vaccine candidates after serialpassages in Vero cells (4-74% reversion by P10). This suggests that thisstrategy for large scale manufacturing of the DENVax seeds issuccessful, regarding maintaining genetic stability and retention ofattenuation markers in the candidate vaccine viruses.

Since MVS stocks disclosed herein will be used for future manufacturingof WVS and BVS lots, full panels of virus attenuation phenotypeevaluations, including small plaque phenotype, temperature sensitivity,reduced replication in mosquito cells, reducedinfection/dissemination/transmission in whole mosquitoes, and reducedneurovirulence in newborn ICR mice, were conducted for all MVS or theirequivalent surrogate stocks. For the WVS and BVS stocks, plaque size,infectivity in mosquito cells, were also performed to confirm theirattenuations. Results indicated that all the MVS stocks of the 4serotypes of DENVax retained the expected attenuation phenotypes, suchas small plaques, reduced replication in C6/36 cells, and reduced mouseneurovirulence, similar to the original lab-derived vaccine viruses(FIGS. 6, 8, and 9). Except for the DENVax-4, all other 3 MVS stocks ofDENVax were TS at 39° C. as shown in FIGS. 3 and 7.

For the WVS and BVS stocks, two attenuation phenotypes, small plaquesand restricted replication in C6/36 cells, were analyzed and confirmed.Since there are very little genetic changes between the MVS and BVS, itwas expected that they would retain the attenuation phenotypes as MVS.In addition to the experiments described in this report, safety andimmunogenicity of the manufactured DENVax in Ag129 mice and nonhumanprimate have been tested.

Exemplary methods are provided herein to demonstrate manufacture ofDENVax MVS, WVS, and BVS stocks under cGMP. The BVS stocks were used toformulate the tetravalent DENVax currently in human clinical trialevaluations. A unique manufacture strategy to optimize the geneticstability and safety of the manufactured MVS was provided in someexemplary methods. Since the main attenuation loci of the DENVax havebeen well characterized previously and a highly sensitive andquantifiable SNP assay, TaqMAMA was developed to integrate genomesequence and the TaqMAMA to identify optimal pre-master seeds for makingthe MVS. The genetic and phenotypic characterizations of the MVS werefully analyzed to confirm that these viruses retained desirableattenuations for safety of the vaccine. This may be the only live,attenuated viral vaccine that can be efficiently analyzed for all themajor attenuation genetic loci during manufacturing from pre-master allthe way to BVS stocks. Results provided herein exemplified the advantageof strategically designed live-attenuated vaccines in vaccine safety.

FIG. 10 represents an exemplary table comparing new live, attenuatedviruses to previously generated live, attenuated dengue viruses.Mutations are indicated where different from a control virus (e.g.16681), or other live, attenuated dengue-2 viruses.

Materials and Methods

Viruses and Cells

DENV-1 16007, DENV-2 16681, DENV-3 16562, and DENV-4 1034 served aswild-type (wt) DENV controls, and they were the parental genotypeviruses for the four recombinant DENVax vaccine candidates. DENVaxprogenitor research-grade viruses, designated as D2/1-V, D2PDK-53-VV45R, D2/3-V, and D2/4-V, were prepared and characterizedpreviously. Vero (African green monkey kidney) cells used for making themaster and working cell banks for vaccine production were originatedfrom the American Type Culture Collection (ATCC) CCL81 cell line thathas been characterized by the World Health Organization (WHO) forvaccine manufacture (WCB-Vero cells).

Derivation of Live Recombinant DENVax Viruses from cDNA Clones

To re-derive the candidate vaccine viruses under cGMP manufacturingconditions, the previously engineered DENV infectious cDNA clones,pD2-PDK-53-VV45R, pD2/1-V, pD2/4-V, and in vitro-ligated pD2/3-Vcontaining the full genome-length viral cDNAs were used to make freshviral RNA transcripts by in vitro transcription as described previously.Briefly, XbaI-linearized DENV genomic cDNAs were treated with proteinaseK, extracted with phenol/chloroform and precipitated in ethanol toremove any residual proteins, and then suspended in RNase-free Tris-EDTAbuffer prior to transcription. The in vitro transcription was conductedusing the AmpliScribe T7 High Yield Transcription kit (EpicentreTechnologies) following the manufacturer's recommended protocol. The RNAA-cap analog, m7G(5′)ppp(5′)A (New England BioLabs), was incorporatedduring the 2-hr transcription reaction to add the 5′-terminal A-cap tothe RNA transcript. The samples were then treated with DNase I to digestthe template cDNA, followed by low pH phenol/chloroform extraction andethanol precipitation to remove residual DNA and proteins. The purifiedRNA transcripts, suspended in RNase-free water, were distributed in20-μl aliquots and stored at −80° C. until ready for transfection ofcells. The integrity and concentration of the RNA transcripts wereanalyzed by agarose gel electrophoresis. Each 20-μl aliquot wasestimated to contain sufficient genome-length viral RNA to permittransfection of 0.4-1×10⁷ production-certified Vero cells byelectroporation.

Transfection of each RNA transcript into WCB-Vero cells was performed inthe cGMP facility at Shantha Biotechnics. DENVax RNA transcripts werethawed, mixed with 400 μl of the Vero cell suspension (1×10⁷ cells/ml),and transferred to a pre-chilled sterile electroporation cuvette (4-mmgap) for electroporation by a Gene Pulser Xcell total system (BioRadLaboratories). Each sample was pulsed once at 250V/∞ Ohms/500 μF,incubated for 10-15 min at room temperature, transferred to a 75-cm²flask containing 30 ml of cell growth medium (MEM with 10% FBS), andincubated at 36° C.±1° C., 5% CO₂ for 6 to 11 days. The culture mediumwas harvested, clarified by centrifugation, stabilized, and stored insmall aliquots below −60° C. The viral titers of candidate vaccinestocks (termed P1 for passage level 1) resulting from transfection weredetermined by plaque titration assay in Vero cells and used for furtherpropagation of the DENVax seeds.

Manufacture of DENVax Virus Seeds

P1 virus seeds were used to propagate DENVax pre-master, master,working, and bulk virus seed lots through a strategy designed to ensurethe optimal genetic stability and safety of the manufactured lots. Thisstrategy included three serial plaque purifications, as well as geneticanalyses of viruses at various passage levels to select the optimalclonal virus population for continued seed production (Table 1).Briefly, the P1 seeds harvested from transfected cells were amplifiedonce by infection of Vero cells at a MOI of 0.001 to generate the P2seeds. Aliquots of the P2 seed stocks were evaluated by plaquemorphology and complete viral genomic sequencing. The geneticallyconfirmed P2 stocks were plated on Vero cell monolayers with overlaymedium as described in the plaque titration section below to generatewell-isolated plaques. After visualization with neutral red, sixindividual plaques from each of the 4 serotypes of vaccine viruses wereisolated (plaque clones A to F) and mixed into 0.5 ml of culture medium(passage P3). Each of the six plaque suspensions was subjected to twoadditional rounds of plaque purification, resulting in twice- andthrice-plaque purified virus seeds at passages P4 and P5, respectively.The P5 viruses were amplified through two sequential Vero passages toproduce P7 seed stocks.

Genetic analysis of the three major DENVax attenuation loci using spotsequencing and/or Taqman-based mismatched amplification mutation assay(TaqMAMA) as previously disclosed, and plaque phenotype analysis wereconducted to screen all 24 P7 seeds. Seeds possessing appropriateinitial characteristics were then further characterized by full genomicsequencing. As a result of these analyses, one of the 6 (clone A-F) P7seeds of each DENVax serotype was selected to be the pre-master seed,based on the presence of the DENV-2 PDK-53 attenuating mutations,minimal genomic sequence alterations, and expected plaque phenotype.Each selected pre-master seed was expanded to master virus seed (MVS orP8) by a one-time passage of the virus at MOI of 0.001M multiple 175 cm²flasks of Vero cells. Except for the DENVax-4 MVS, the master virusseeds were harvested at 8-10 days post infection (pi). The MVS stockswere harvested at 6-10 days post infection (pi), clarified bycentrifugation, stabilized by the addition ofsucrose/phosphate/glutamate solution (final concentration 7.5% sucrose,3.4 mM potassium dihydrogen phosphate, 7.2 mM dipotassium hydrogenphosphate, 5.4 mM monosodium glutamate, respectively) and 0.95 to 1.90%FBS (final concentration). DENVax-4 MVS was prepared differently tooptimize its yield. Briefly, multiple flasks of cells were infected withDENVax-4 pre-master seed at a MOI of 0.001 in the presence of 0.1%F-127™, poloxamer 407, (other EO-PO block copolymers have been assessedand may substitute here, see issued patent) that have been demonstratedto enhance DENV virus thermal stability. Infectious media was harvesteddays 6-10 pi, and stabilized with 17% FBS (final concentration), pooled,and frozen. All four DENVax MVS stocks were stored as 1-ml aliquotsbelow −60° C.

The DENVax working virus seeds (WVS) were prepared by one-time passagein Vero cell culture of the MVS at a MOI of 0.001. The procedures weresimilar to the production of MVS, except they were cultured inmultiple-layer cell factories (6360 cm²). The WVS stocks were filteredthrough 10 μM and 0.45 μM filters, stabilized with the same stabilizersused for the MVS, aliquoted into 30 ml PETG bottles or 2.0 ml cryovials,and stored below −60° C.

In certain methods, bulk virus seeds (BVS) were produced by infectingmultiple cell factories (6360 cm² each) of confluent Vero cells with 90mL of diluted WVS to attain a MOI of 0.001. A media used for dilution ofthe WVS inocula contained 0.1% F-127™ without serum. After 1.5 hradsorption, cells were washed 3 times with PBS, and 800 ml of serum-freeDMEM medium was added to each cell factory, and the factories wereincubated at 36(±1°) C. in 5(±0.5)% CO₂. After incubation for four days,small aliquots of medium were collected for sterility testing. Viruseswere harvested between day 5 and day 10 pi, and immediately clarified byfiltration through a 0.45 um pore size filter, and 1 L of each clarifiedvirus pool was stabilized by addition of 500 ml of 3×FTA buffer (finalconcentrations of 15% trehalose, 1.0% Pluronic® F-127™ poloxamer 407,0.1% human albumin USP in PBS, pH 7.4). The stabilized virus wasdistributed into 1-L PETG bottles and stored frozen below −60° C. forsubsequent pooling and quality control testing. All stabilized virusharvests with a virus titer above 10⁵ PFU/ml and an acceptable level ofresidual DNA were rapidly thawed in a water bath at 32° C., thenaseptically pooled and mixed. Each pooled monovalent BVS was distributedinto labeled PETG containers and stored at below −60° C. until furtheruse.

Manufacture Product Quality Controls

The MVS, WVS, and BVS seeds were tested for identity, sterility, anddetectable adventitious agents. The identity of each vaccine stock wasconfirmed by RT-PCR with DENVax serotype-specific primers. The amplifiedcDNA fragments contained the E/NS1 chimeric junction site to permitidentification of each of the four DENVax serotypes. Each seed wastested in all 4 serotype-specific RT-PCR reactions to confirm viralidentity and freedom from cross contamination with heterologous DENVaxserotypes. Sterility testing was performed in accordance with USP 71(United States Pharmacopeia, section 71). Mycoplasma testing wasperformed.

The following in vitro and in vivo tests for viral contamination wereall performed using unclarified, unstabilized DENVax harvests collectedduring manufacture of the seeds. Harvested infectious media were firstneutralized with DENV rabbit polyclonal antiserum (Inviragen) at 36±1°C. for 1 hr to inactivate the DENV. For in vitro test, the neutralizedseeds were inoculated into three indicator cells lines, MRCS, VERO andMA104, in 25 cm² flasks. Echo virus (CPE control) or mumps virus(hemadsorption control) were used as positive CPE or hemadsorptioncontrol, respectively. All cells were monitored daily for CPE for atotal of 14 days. At the end of 14 days, the culture supernatant wasremoved and replaced with 10 mL of a guinea pig red blood cell (RBC)solution (3 mL of 0.5% guinea pig RBC in phosphate buffered saline, madeup to 10 mL with cell growth medium). The flasks were then incubated at5±3° C. for 30 minutes followed by incubation at room temperature for 30minutes. The monolayers were washed with PBS and observed under 10×magnification for the presence of any star-shaped clumps of RBCs forhemadsorption.

In vivo tests for adventitious agents were performed in suckling mice,post-weaning mice and guinea pigs. Suckling mice were inoculated with0.1 ml or 0.01 ml (10 mice in each dose group) of the DENV-antiserumneutralized seed sample through intraperitoneal (ip) injection.Similarly, 10 post-weaning mice were each inoculated ip with 0.5 ml or0.03 ml of the sample. Guinea pigs (5/group) were each inoculated ipwith 5.0 mL. Suckling mice were observed daily for morbidity andmortality for a total of 14 days following inoculation. Post-weaningmice were observed for a total of 28 days, and guinea pigs were observedfor a total of 42 days following inoculation. The test articles met theacceptance criterion if ≥80% of the inoculated animals remained healthythroughout the observation period.

The in vivo testing for contaminants was also performed in embryonatedchicken eggs and was conducted. For every sample, 10 embryonated heneggs (9 days old) were each inoculated with 0.5 mL of the DENVantiserum-neutralized sample into the allantoic fluid and incubated at35° C. for 3 days. The allantoic fluids from these 10 eggs wereharvested, pooled and passaged into the allantoic fluid of 10 freshembryonated eggs (10-11 days old; 0.5 mL/egg) and incubated at 35° C.for a further 3 days. Similarly, for each sample, 10 embryonated eggs(6-7 days old) were each inoculated with 0.5 mL per egg (DENVax-2monovalent BVS) or 0.25 mL per egg (DENVax-1, DENVax-3 and DENVax-4 BVS)by injection into the yolk sac and incubated at 35° C. for 9 days. Theyolk sacs from these 10 eggs were harvested and pooled, and a 10%suspension was passaged into the yolk sacs of 10 fresh embryonated eggs(6-7 days old; 0.5 mL/egg) and incubated at 35° C. for a further 9 days.Eggs inoculated into the allantoic fluid (both initial and passageinoculations) were observed for viability after 3 days incubation. Bothpools of allantoic fluid were tested for hemagglutination activity usingchicken, guinea pig and human type O erythrocytes at 4° C. and 25° C.Eggs inoculated into the yolk sack (both initial and passageinoculations) were observed for viability after 9 days of incubation.

Virus Plaque Assay and Immunofocus Assay

Virus titers were measured by plaque assay or immunofocus assay usingVero cells. Plaque assays were performed in double agarose overlays insix-well plates of confluent Vero cells as previously described, andthey were also used to evaluate the plaque phenotypes of the DENVaxseeds. For accurate comparison, plaque sizes of all viruses weremeasured and compared in the same experiment. After visualization withneutral red on day 9 pi, up to 10 well isolated plaques for each viruswere measured for mean plaque size calculation. Fewer plaques weremeasured for wt DENV-1, -3, and -4, whose larger plaque sizes often didnot permit measurement of 10 well-separated plaques.

Because tetravalent DENVax contains all four DENV serotypes, a DENVserotype-specific immunofocus assay was developed to quantitate eachDENVax component in the tetravalent formulations Immunofocus assays ofeach individual DENVax MVS were compared with the plaque assays toensure virus titration results were comparable between the two assays.The immunofocus assay was conducted in 6-well plates of confluent Verocells infected with serially diluted viruses. Cells were overlayed witha balanced salt medium (BSS/YE-LAH medium) containing 0.7% highviscosity carboxymethyl cellulose (Sigma) and incubated for 7 days at37° C. with 5% CO₂. After removal of overlays, cell sheets were washed 3times with PBS, fixed with cold 80% acetone for 30 min at −20° C.,washed once with PBS, and blocked with a blocking buffer containing 2.5%(w/v) nonfat dry milk, 0.5% Triton X-100, 0.05% Tween-20 in PBS at 37°C. for 30 min. Blocked cells were incubated with diluted DENVserotype-specific MAbs, 1F1 (DENV-1), 3H5 (DENV-2), 8A-1 (DENV-3), or1H10 (DENV-4) in blocking buffer at 37° C. for 1 hour or 4° C.overnight, washed 3 times with washing buffer (0.05% Tween-20 in PBS),and incubated with alkaline phosphatase- or horse radish peroxidase(HRP)-conjugated affinity-pure goat anti-mouse IgG (Jackson ImmunoResearch Laboratories) at 37° C. for 45-60 min. Plates were washed 3times before the appropriate substrate, 1-Step NBT/BCIP plus suppressor(Pierce) for alkaline phosphatase or Vector-VIP kit (Vector Labs) forHRP, was added for color development. Color development was stopped byrinsing with water when the foci were fully developed. Stainedimmunofoci were directly visualized and counted on a light box.

Genetic Sequence

Full length genomes of the MVS and WVS were sequenced (see below).Briefly, viral RNA was extracted from DENVax seeds by using the QIAampviral RNA kit (Qiagen), and overlapping cDNA fragments covering theentire genome were amplified using the Titan One Tube RT-PCR kit (RocheApplied Science, Inc.). The amplified cDNA fragments were gel purifiedbefore sequencing with both forward and reverse primers using the BigDyeTerminator v3.1 cycle sequencing kit (Applied Biosystems). Sequencereactions were cleaned using the BigDye XTerminator Purification kit(Applied Biosystems), and run on the 3130xl Genetic analyzer (AppliedBiosystems) at DVBD/CDC. The Lasergene SeqMan software (DNAStar, Inc)was used for genome analysis and comparison.

Taqman-based Mismatch Amplification Mutation Assay (TaqMAMA)

TaqMAMA is a sensitive, quantitative single nucleotide polymorphismassay developed to permit finer assessment of the level of reversion atthe 5′NC-57 locus of attenuation, and was further optimized for thisstudy. Extracted viral RNA from MVS and WVS were analyzed by the TaqMAMAwith both sets of primers/Taqman probe that are specific to wt or thevaccine 5′NC-57 region. The forward primers used to detect DENV-2 wt andvaccine sequences were D2-41-GC and D2-40-TT, respectively. The3′-terminal nucleotide of each forward primer matched the specific5′NCR-57 nucleotide for each virus, while the nucleotide adjacent to the3′-terminal nucleotide in each primer differed from the DENV-2 viralgenomic sequence to enhance the mismatch effect. The reverse primer,CD-207, and the Taqman probe, CD-169F, for both wt and vaccine sets wereidentical. Sequences of the primers and probe as well as cyclingconditions were described previously. The real time RT-PCR was performedwith the iQ5 or CFX-95 system (BioRad), using a BioRad iScript RT-PCR(for probes) kit, in a 25-μl reaction containing 5 μl of viral RNAtemplate, 0.4 uM of each primer, and 0.2 uM of the probe. Triplicatereactions for each wt- and vaccine-specific assay were conducted foreach sample. Genome copy numbers were determined relative to a standardcurve prepared for each viral genotype, where the RNA standards weretranscripts derived from plasmids containing nt 1-2670 of eachgenotype-specific cDNA. In addition, the specificity of the assay wasconfirmed by testing each RNA standard with the heterologous genotypeprimer/probe sets to ensure minimum cross-reactivity in everyexperiment. The results were reported as the percentage of viral genomesshowing reversion. Previously, due to higher cross-reactive backgroundsthat limited the input RNA levels for this assay, the original detectionsensitivity was about 0.1% reversion (discrimination power). Since then,the assay has been further optimized using improved real-time PCRequipment and reaction kits, and the cross-reactive background wasdecreased considerably at much high levels (7-8 log₁₀ copies) of RNAtemplate input. This optimization resulted in significant improvement ofthe detection sensitivity, down to 0.01-0.07% reversion.

Virus Replication in Mosquito C6/36 Cells and Temperature Sensitivity inMammalian Vero Cells

The replication phenotypes of the four DENVax MVS stocks and wt DENV-1,-2, -3, and -4 viruses were evaluated in C6/36 mosquito cells (Aedesalbopictus). C6/36 cells grown in 6-well plates were infected induplicate with each virus at a MOI of 0.001 and incubated with 4 ml/wellof DMEM medium containing 2% FBS in a 5% CO₂ incubator at 28° C. Smallaliquots of the culture supernatant were collected for each virus on day6 pi, mixed with an equal volume of medium containing 40% FBS, andstored at −80° C. until ready for virus plaque titration.

Temperature sensitivity was conducted by comparing viral growth at 39°C. versus growth at 37° C. at five days pi of Vero cells in 6-wellplates. Cells were infected in quadruplicate with each virus at a MOI of0.001 at 37° C. Following adsorption of virus, the infected cultureswere incubated with 4 ml/well of DMEM medium containing 2% FBS in 2separate 5% CO₂ incubators, one set (duplicate plates) at 37° C. and theother at 39° C. Aliquots (50-μl) of the culture supernatant werecollected on day 5 pi, mixed with an equal volume of DMEM containing 40%of FBS, and stored at −80° C. until ready for virus plaque titration.Incubator temperatures were calibrated with NIST-traceablefactory-calibrated thermometers (−1 to 51° C.; ERTCO).

Mosquito Infection, Dissemination, and Transmission

Aedes aegypti mosquitoes used for the study were from a colonyestablished in 2002 from a village near Mae Sot (16′ N, 33′ E),Thailand. After emerging from larvae, adult mosquitoes were maintainedat 28° C. at a 16:8 (light:dark) photoperiod with 10% sucrose solutionprovided ad libitum. Five-to-seven day old female mosquitoes were usedfor infectious blood meal feeding or intrathoracic (IT) inoculations.Aliquots of freshly cultured DENVax and wt DENV were used immediatelyupon harvest (without any freeze-thaw cycle) to make virus blood mealsas indicated below for oral infection. Remaining virus supernatants weresupplemented with FBS to a final concentration of 20%, and aliquots werestored at −80° C. for future virus plaque titration and IT inoculationexperiments. The freshly prepared DENVax seeds for these experimentswere amplified from the pre-master seeds in Vero cells, and wereconsidered DENVax MVS equivalents.

Infectious blood meals were prepared by mixing fresh virus at a ratio of1:1 with defribrinated chicken blood (Colorado Serum Company) on the dayof oral infection. Mosquitoes were sugar-starved overnight and thenoffered the virus:blood mixture for 1 hour using a Hemotek membranefeeding system (Discovery Workshops). A 50-μl aliquot of the blood mealwas retained at −80° C. for back-titration of virus doses.Fully-engorged females were sorted under cold anesthesia and placed intocartons with 10% sucrose solution provided ad libitum. Cartons wereplaced at 28° C. with a photoperiod of 16:8 h (light:dark). After 14days, 25-30 mosquitoes from each virus group were anesthetized viaexposure to triethylamine (Flynap®, Carolina Biological Supply Company)and one hind leg was removed and placed in 0.5 ml of DMEM with 10% FBSand 5% penicillin/streptomycin (100 U/ml and 100 μg/ml respectively).Saliva was collected by inserting the proboscis of the anesthetizedmosquito into a capillary tube containing 2.5% FBS and 25% sucrosesolution. Mosquitoes were allowed to salivate for at least 15 minutesand then capillary tubes and bodies were placed into separate tubescontaining DMEM. Mosquito bodies, legs and saliva were stored at −80° C.until they were triturated and assayed for infectious virus. For ITinoculation, mosquitoes were cold-anesthetized and inoculated withapproximately 50 pfu of virus in 0.34 μl inoculum. Inoculated mosquitoeswere kept for 7 days in the same conditions as described above.Mosquitoes were then anesthetized, and their saliva and bodies werecollected as described above. Samples were stored at −80° C. untilfurther processing.

To process the samples for virus titration, body and leg samples werehomogenized with copper coated BBs (Crossman Corporation, NY) at 24cycles/second for 4 min using a mixer mill, and then clarified bycentrifuging at 3,000× g for 3 min. Saliva samples were centrifuged at3,000× g for 3 minutes to expel fluid from capillary tubes. Ten-folddilutions of the body and leg homogenates and saliva samples were testedfor presence of infectious virus by plaque assay. Results from bodies,legs, and saliva were used for determining the infection, dissemination,and transmission rates, respectively.

Mouse Neurovirulence

Timed pregnant female ICR mice were obtained from Taconic Labs, andmonitored several times each day to determine approximate birth times ofpup litters. In a given experiment, approximately 12-24 hours afterbirth, two litters of eight pups per virus (n=16), was challenged with10³ to 10⁴ pfu of virus in 20 μl of diluent by intracranial (ic)inoculation using a 30-gauge needle Animals were monitored at least 3times daily for at least 32 days following challenge. At the first signof illness (rough fur, hunched back, weight loss, abnormal movement,paralysis, or lethargy) animals were euthanized by lethalanesthetization with isoflurane gas, followed by cervical dislocation.The post-infection day of euthanasia represented the “time toillness/morbidity” or “survival time” for the animal. The animalexperiments were conducted following a DVBD/CDC IACUC-approved animalprotocol.

Derivation of Master Seed Viruses

DENvax-1 Master Virus Seed (MVS)

Nucleotide sequence of the chimeric viral genome and deduced amino acidsequence of the translated protein are provided herein. Most of theprM-E gene (nt 457 to -2379, underlined) is wild-type (wt) DEN-1 16007virus specific; the remaining genome is DEN-2 PDK-53 virus specific. Allengineered substitutions differ from wt virus (D1 16007 or D2 16681), aswell as extra mutations (changes from engineered cDNA clone) detected inthe MVS are marked.

Substitutions Included in the Genome and Protein:

Junction sites between D1 (prM-E) and D2 backbone:

-   -   a. MluI (nt 451-456): engineered silent mutation, nt-453 A-to-G    -   b. NgoMIV (nt 2380-2385): engineered mutations, nt-2381/2382        TG-to-CC (resulted in E-482 Val-to-Ala change)

D2 PDK-53 virus backbone (change from wt D2 16681): all in bold

-   -   a. 5′-noncoding region(NCR)-57 (nt-57 C-to-T): major attenuation        locus (in red)    -   b. NS1-53 Gly-to-Asp (nt-2579 G-to-A): major attenuation locus        (in red)    -   c. NS2A-181 Leu-to-Phe (nt-4018 C-to-T)    -   d. NS3-250 Glu-to-Val (nt-5270 A-to-T): major attenuation locus        (in red)    -   e. nt-5547 (NS3 gene) T-to-C silent mutation    -   f. NS4A-75 Gly-to-Ala (nt-6599 G-to-C)    -   * nt-8571 C-to-T silent mutation of PDK-53 is not engineered in        the vaccine virus

DEN-1 prM-E (change from wt D1 16007)

-   -   a. Engineered nt-1575 T-to-C silent mutation to remove native        XbaI site

Additional substitutions found in vaccine seed (0.03% nt different fromoriginal clone)

-   -   a. NS2A-116 Ile-to-Leu (nt-3823 A-to-C, in bold)    -   b. NS2B-92 Glu-to-Asp (nt-4407 A-to-T, in bold)    -   c. nt-7311 A-to-G silent mutation (in bold)

                                        NCR-57-T. D2 PDK-53 attenuation locus (wt D2 16681: C) >5′-Noncoding Region                                   |                                       >C         10        20        30        40        50        60        70        80        90       100 AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAATGTAGTTCTAACAGTTTTTTAATTAGAGAGGAGATCTCTGATGA                                                                                                 M  N        110       120       130       140       150       160       170       180       190       200 ATAACCAACGGAAAAAGGCGAAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACT   N  Q  R  K  K  A  K  N  T  P  F  N  M  L  K  R  E  R  N  R  V  S  T  V  Q  Q  L  T  K  R  F  S  L        210       220       230       240       250       260       270       280       290       300 TGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGGAGGGATATTGAAGAGA  G  M  L  Q  G  R  G  P  L  K  L  F  M  A  L  V  A  F  L  R  F  L  T  T  P  P  T  A  G  I  L  K  R        310       320       330       340       350       360       370       380       390       400 TGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTG W  G  T  I  K  K  S  K  A  T  N  V  L  R  G  E  R  K  E  T  G  R  M  L  N  T  L  N  R  R  R  R  S  A                                       >prM                 Beginning of D1 16007 sequence        410       420       430       440       450       |460       470       480       490       500 CAGGCATGATCATTATGCTGATTCCAACAGTGATGGCGTTCCATTTAACCAC

CGT GGGGGAGAGCCGCATATGATAGTTAGCAAGGAGGAAAGAGGAAA   G  M  T  T  M  L  I  P  T  V  M  A  F  H  L  T  T  R  G  G  E  P  H  M  T  V  S  K  Q  E  R  G  K      |                                                Engineered MluI splicing site (nt-453 A-to-G silent)        520       530       540       550       560       570       580       590       600 GTCACTTTTGTTCAAGACCTCTGCAGGTGTCAACATGTGCACCCTCATTGCGATGGATTTGGGAGAGTTGTGTGAGGACACGATGACCTACAAATGCCCC  S  L  L  F  K  T  S  A  G  V  N  M  C  T  L  T  A  M  D  L  G  E  L  C  E  D  T  M  T  Y  K  C  P        610       620       630       640       650       660       670       680       690       700 CGGATCACTGAGGCGGAACCAGATGACGTTGACTGTTGGTGCAATGCCACGGACACATGGGTGACCTATGGAACGTGCTCTCAAACTGGCGAACACCGAC R  T  T  E  A  E  P  D  D  V  D  C  W  C  N  A  T  D  T  W  V  T  Y  G  T  C  S  Q  T  G  E  H  R  R  >M        710       720       730       740       750       760       770       780       790       800 GAGACAAACGTTCCGTCGCATTGGCCCCACACGTGGGGCTTGGCCTAGAAACAAGAGCCGAAACGTGGATGTCCTCTGAAGGTGCTTGGAAACAGATACA   D  K  R  S  V  A  L  A  P  H  V  G  L  G  L  E  T  R  A  E  T  W  M  S  S  E  G  A  W  K  Q  T  Q        810       820       830       840       850       860       870       880       890       900 AAAAGTAGAGACTTGGGCTCTGAGACATCCAGGATTCACGGTGATAGCCCTTTTTCTAGCACATGCCATAGGAACATCCATCACCCAGAAAGGGATCATT  K  V  E  T  W  A  L  R  H  P  G  F  T  V  T  A  L  F  L  A  H  A  T  G  T  S  T  T  Q  K  G  I  I                                     >E        910       920       930       940       950       960       970       980       990      1000 TTCATTTTGCTGATGCTGGTAACACCATCTATGGCCATGCGATGCGTGGGAATAGGCAACAGAGACTTCGTGGAAGGACTGTCAGGAGCAACATGGGTGG F  I  L  L  M  L  V  T  P  S  M  A  M  R  C  V  G  I  G  N  R  D  E  V  E  G  L  S  G  A  T  W  V  D       1010      1020      1030      1040      1050      1060      1070      1080      1090      1100 ATGTGGTACTGGAGCATGGAAGTTGCGTCACCACCATGGCAAAAAACAAACCAACACTGGACATTGAACTCTTGAAGACGGAGGTCACAAACCCTGCAGT   V  V  L  E  K  G  S  C  V  T  T  M  A  K  N  K  P  T  L  D  T  E  L  L  K  T  E  V  T  N  P  A  V       1110      1120      1130      1140      1150      1160      1170      1180      1190      1200 TCTGCGTAAATTGTGCATTGAAGCTAAAATATCAAACACCACCACCGATTCGAGATGTCCAACACAAGGAGAAGCCACACTGGTGGAAGAACAAGACGCG  L  R  K  L  C  T  E  A  K  T  S  N  T  T  T  D  S  R  C  P  T  Q  G  E  A  T  L  V  E  E  Q  D  A       1210      1220      1230      1240      1250      1260      1270      1280      1290      1300 AACTTTGTGTGCCGACGAACGTTCGTGGACAGAGGCTGGGGCAATGGCTGTGGGCTATTCGGAAAAGGTAGTCTAATAACGTGTGCCAAGTTTAAGTGTG N  F  V  C  R  R  T  F  V  D  R  G  W  G  N  G  C  G  L  F  G  K  G  S  L  I  T  C  A  K  F  K  C  V       1310      1320      1330      1340      1350      1360      1370      1380      1390      1400 TGACAAAACTAGAAGGAAAGATAGTTCAATATGAAAACCTAAAATATTCAGTGATAGTCACCGTCCACACTGGAGATCAGCACCAGGTGGGAAATGAGAC   T  K  L  E  G  K  I  V  Q  Y  E  N  L  K  Y  S  V  I  V  T  V  H  T  G  D  Q  H  Q  V  G  N  E  T       1410      1420      1430      1440      1450      1460      1470      1480      1490      1500 TACAGAACATGGAACAACTGCAACCATAACACCTCAAGCTCCTACGTCGGAAATACAGCTGACCGACTACGGAACCCTTACATTAGATTGTTCACCTAGG  T  E  H  G  T  T  A  T  I  T  P  Q  A  P  T  S  E  I  Q  L  T  D   Y  G  T  L  T  L  D  C  S  P  R       1510      1520      1530      1540      1550      1560      1570      1580      1590      1600 ACAGGGCTAGATTTTAACGAGATGGTGTTGCTGACAATGAAAGAAAGATCATGGCTTGTCCACAAACAATGGTTCCTAGACTTACCACTGCCTTGGACCT T  G  L  D  F  N  E  M  V  L  L  T  M  K  E  R  S  W  L  V  H  K  Q  W  F  L  D  L  P  L  P  W  T  S                                                                           |Engineered silent mutation (nt-1575 T-to-C): remove the native DEN-1 virus-specific xbaI site       1610      1620      1630      1640      1650      1660      1670      1680      1690      1700 CTGGGGCTTCAACATCCCAAGAGACTTGGAACAGACAAGATTTACTGGTCACATTTAAGACAGCTCATGCAAAGAAGCAGGAAGTAGTCGTACTAGGATC   G  A  S  T  S  Q  E  T  W  N  R  Q  D  L  L  V  T  F  K  T  A  H  A  K  K  Q  E  V  V  V  L  G  S       1710      1720      1730      1740      1750      1760      1770      1780      1790     1800 ACAAGAAGGAGCAATGCACACTGCGCTGACTGGAGCGACAGAAATCCAAACGTCAGGAACGACAACAATTTTCGCAGGACACCTAAAATGCAGACTAAAA  Q  E  G  A  M  H  T  A  L  T  G  A  T  E  I  Q  T  S  G  T  T  T  I  F  A  G  H  L  K  C  R  L  K       1810      1820      1830      1840      1850      1860      1870      1880      1890      1900 ATGGACAAACTAACTTTAAAAGGGATGTCATATGTGATGTGCACAGGCTCATTCAAGTTAGAGAAAGAAGTGGCTGAGACCCAGCATGGAACTGTTCTGG M  D  K  L  T  L  K  G  M  S  Y  V  M  C  T  G  S  F  K  L  E  K  E  V  A  E  T  Q  H  G  T  V  L  V       1910      1920      1930      1940      1950      1960      1970      1980      1990      2000 TGCAGGTTAAATATGAAGGAACAGACGCACCATGCAAGATTCCCTTTTCGACCCAAGATGAGAAAGGAGCAACCCAGAATGGGAGATTAATAACAGCCAA   Q  V  K  Y  E  G  T  D  A  P  C  K  I  P  F  S  T  Q  D  E  K  G  A  T  Q  N  G  R  L  I  T  A  N       2010      2020      2030      2040      2050      2060      2070      2080      2090      2100 CCCCATAGTCACTGACAAAGAAAAACCAGTCAATATTGAGGCAGAACCACCCTTTGGTGAGAGCTACATCGTGGTAGGAGCAGGTGAAAAAGCTTTGAAA  P  I  V  T  D  K  E  K  P  V  N  T  E  A  E  P  P  F  G  E  S  Y  I  V  V  G  A  G  E  K  A  L  K       2110      2120      2130      2140      2150      2160      2170      2180      2190      2200 CTAAGCTGGTTCAAGAAAGGAAGCAGCATAGGGAAAATGTTTGAAGCAACTGCCCGAGGAGCACGAAGGATGGCCATTCTGGGAGACACCGCATGGGACT L  S  W  F  K  K  G  S  S  I  G  K  M  F  E  A  T  A  R  G  A  R  R  M  A  I  L  G  D  T  A  W  D  F       2210      2220      2230      2240      2250      2260      2270      2280      2290      2300 TCGGTTCTATAGGAGGAGTGTTCACGTCTATGGGAAAACTGGTACACCAGGTTTTTGGAACTGCATATGGAGTTTTGTTTAGCGGAGTTTCTTGGACCAT   G  S  I  G  G  V  E  T  S  M  G  K  L  V  H  Q  V  F  G  T  A  Y  G  V  L  F  S  G  V  S  W  T  M                                                                       End of D1 16007 sequence                                                                                |      2310      2320      2330      2340      2350      2360      2370      2380      2390      2400 GAAAATAGGAATAGGGATTCTGCTGACATGGCTAGGATTAAATTCAAGGAACACGTCCCTTTCGATGATGTGCATCGCAGCCGGCATTGTGACACTGTAT  K  I  G  I  G  I  L  L  T  W  L  G  L  N  S  R  N  T  S  L  S  M  M  C  I  A  A  G  I  V  T  L  Y                                                                                |                           Engineered NgoMIV splicing site, E-482 Val-to-Ala (nt-2381/2382 TG-to-CC)                      >NS1       2410      2420      2430      2440      2450      2460      2470      2480      2490      2500 TTGGGAGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACA L  G  V  M  V  Q  A  D  S  G  C  V  V  S  W  K  N  K  E  L  K  C  G  S  G  I  F  I  T  D  N  V  H  T       2510      2520      2530      2540      2550      2560      2570      2580      2590      2600 CATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGACATTTGTGGAATCCGCTCAGT   W  T  E  Q  Y  K  F  Q  P  E  S  P  S  K  L  A  S  A  I  Q  K  A  H  E  E  D  I  C  G  I  R  S  V                                                                              |                          D2 PDK-53 attenuation locus (wt. D2 16681: Gly, nt-2579-G)      2610      2620      2630      2640      2650      2660      2670      2680      2690      2700 AACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCAGAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATC  T  R  L  E  N  L  M  W  K  Q  I  T  P  E  L  N  H  I  L  S  E  N  E  V  K  L  T  I  M  T  G  D  I       2710      2720      2730      2740      2750      2760      2770      2780      2790      2800 AAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTATTCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAG K  G  I  M  Q  A  G  K  R  S  L  R  P  Q  P  T  E  L  K  Y  S  W  K  T  W  G  K  A  K  M  L  S  T  E       2810     2820      2830      2840      2850      2860      2870      2880      2890      2900 AGTCTCATAACCAGACCTTTCTCATTGATGGCCCCGAAACAGCAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTGGAAGTTGAAGACTATGGCTT   S  H  N  Q  T  F  L  I  D  G  P  E  T  A  E  C  P  N  T  N  R  A  W  N  S  L  E  V  E  D  Y  G  F       2910      2920      2930      2940      2950      2960      2970      2980      2990      3000 TGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAAAAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCC  G  V  F  T  T  N  I  W  L  K  L  K  E  K  Q  D  V  F  C  D  S  K  L  M  S  A  A  I  K  D  N  R  A       3010      3020      3030      3040      3050      3060      3070      3080      3090      3100 GTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAA V  H  A  D  M  G  Y  W  I  E  S  A  L  N  D  T  W  K  I  E  K  A  S  F  I  E  V  K  N  C  H  W  P  K       3110      3120      3130      3140      3150      3160      3170      3180      3190      3200 AATCACACACCCTCTGGAGCAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAACACAACTATAGACCAGGCTA   S  H  T  L  W  S  N  G  V  L  E  S  E  M  I  I  P  K  N  L  A  G  P  V  S  C  H  N  Y  R  P  G  Y       3210      3220      3230      3240      3250      3260      3270      3280      3290      3300 CCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTTGAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAAT  H  T  Q  I  T  G  P  W  H  L  G  K  L  E  M  D  F  D  F  C  C  G  T  T  V  V  V  T  E  D  C  G  N       3310      3320      3330      3340      3350      3360      3370      3380      3390      3400 AGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGG R  G  P  S  L  R  T  T  T  A  S  G  K  L  I  T  E  W  C  C  R  S  C  T  L  P  P  L  R  Y  R  G  E  D                                                                              >NS2A       3410      3420      3430      3440      3450      3460      3470      3480      3490      3500 ATGGGTGCTGGTACGGGATGGAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGACATGGGCAGGTCGACAACTT   G  C  W  Y  G  M  E  I  R  P  L  K  E  K  E  E  N  L  V  N  S  L  V  T  A  G  H  G  Q  V  D  N  F       3510      3520      3530      3540      3550      3560      3570      3580      3590      3600 TTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAAATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTG  S  L  G  V  L  G  M  A  L  F  L  E  E  M  L  R  T  R  V  G  T  K  H  A  I  L  L  V  A  V  S  F  V       3610      3620      3630      3640      3650      3660      3670      3680      3690      3700 ACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGCGCCACTATGACGGATGACATAGGTATGGGCGTGACTTATC T  L  I  T  G  N  M  S  F  R  D  L  G  R  V  M  V  M  V  G  A  T  M  T  D  D  I  G  M  G  V  T  Y  L       3710      3720      3730      3740      3750      3760      3770      3780      3790      3800 TTGCCCTACTAGCAGCCTTCAAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTGATGATGACTACTATAGGAAT   A  L  L  A  A  F  K  V  R  P  T  F  A  A  G  L  L  L  R  K  L  T  S  K  E  L  M  M  T  T  I  G  I       3810      3820      3830      3840      3850      3860      3870      3880      3890      3900 TGTACTCCTCTCCCAGAGCACCCTACCAGAGACCATTCTTGAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAA  V  L  L  S  Q  S  T  L  P  E  T  I  L  E  L  T  D  A  L  A  L  G  M  M  V  L  K  M  V  R  N  M  E  |Additional NS2A-116 Ile-to-Leu (nt3823 A-to-C) mutation in master and pre-master seed       3910      3920      3930      3940      3950      3960      3970      3980      3990      4000 AAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTACAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGG K  Y  C  L  A  V  T  I  M  A  I  L  C  V  P  N  A  V  I  L  Q  N  A  W  K  V  S  C  T  I  L  A  V  V       4010      4020      4030      4040      4050      4060      4070      4080      4090      4100 TGTCCGTTTCCCCACTGTTCTTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCTATTTTTCT   S  V  S  P  L  F  L  T  S  S  Q  Q  K  T  D  W  I  P  L  A  L  T  I  K  G  L  N  P  T  A  I  F  L                  |  D2 PDK-53 specific NS2A-181-Phe (wt. D2 16681: Leu, nt-4018-C)  >NS2B       4110      4120      4130      4140      4150      4160      4170      4180      4190      4200 AACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCATTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAA  T  T  L  S  R  T  S  K  K  R  S  W  P  L  N  E  A  I  M  A  V  G  M  V  S  I  L  A  S  S  L  L  K       4210      4220      4230      4240      4250      4260      4270      4280      4290      4300 AATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAG N  D  I  P  M  T  G  P  L  V  A  G  G  L  L  T  V  C  Y  V  L  T  G  R  S  A  D  L  E  L  E  R  A  A       4310      4320      4330      4340      4350      4360      4370      4380      4390      4400 CCGATGTCAAATGGGAAGACCAGGCAGAGATATCAGGAAGGAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAATGAAGA   D  V  K  W  E  D  Q  A  E  I  S  G  S  S  P  I  L  S  I  T  I  S  E  D  G  S  M  S  I  K  N  E  E       4410      4420      4430      4440      4450      4460      4470      4480      4490      4500 GGAAGATCAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGGAGCATGGTACCTG  E  D  Q  T  L  T  I  L  I  R  T  G  L  L  V  I  S  G  L  F  P  V  S  I  P  I  T  A  A  A  W  Y  L |Additional NS2B-92 Glu-to-Asp (nt-4407 A-to-T) mutation (in master and pre-master seed)                      >NS3       4510      4520      4530      4540      4550      4560      4570      4580      4590      4600 TGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGC W  E  V  K  K  Q  R  A  G  V  L  W  D  V  P  S  P  P  P  M  G  K  A  E  L  E  D  G  A  Y  R  I  K  Q       4610      4620      4630      4640      4650      4660      4670      4680      4690      4700 AAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACACGTGGCGCTGTTCTAATGCA   K  G  I  L  G  Y  S  Q  I  G  A  G  V  Y  K  E  G  T  F  H  T  M  W  H  V  T  R  G  A  V  L  M  H       4710      4720      4730      4740      4750      4760      4770      4780      4790     4800 TAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAA  K  G  K  R  I  E  P  S  W  A  D  V  K  K  D  L  I  S  Y  G  G  G  W  K  L  E  G  E  W  K  E  G  E       4810      4820      4830      4840      4850      4860      4870      4880      4890      4900 GAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCTGGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTAT E  V  Q  V  L  A  L  E  P  G  K  N  P  R  A  V  Q  T  K  P  G  L  F  K  T  N  A  G  T  I  G  A  V  S       4910      4920      4930      4940      4950      4960      4970      4980      4990      5000 CTCTGGACTTTTCTCCTGGAACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGTGTTGTTACAAGGAGTGGAGC   L  D  F  S  P  G  T  S  G  S  P  I  I  D  K  K  G  K  V  V  G  L  Y  G  N  G  V  V  T  R  S  G  A       5010      5020      5030      5040      5050      5060      5070      5080      5090      5100 ATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAAGACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTC  Y  V  S  A  I  A  Q  T  E  K  S  I  E  D  N  P  E  I  E  D  D  I  F  R  K  R  R  L  T  I  M  D  L       5110      5120      5130      5140      5150      5160      5170      5180      5190      5200 CACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAACGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTG H  P  G  A  G  K  T  K  R  Y  L  P  A  I  V  R  E  A  I  K  R  G  L  R  T  L  I  L  A  P  T  R  V  V       5210      5220      5230      5240      5250      5260      5270      5280      5290      5300 TGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGTGCACACCGGGCGGGAGATTGTGGACCTAAT   A  A  E  M  E  E  A  L  R  G  L  P  I  R  Y  Q  T  P  A  I  R  A  V  H  T  G  R  E  I  V  D  L  M                                                                     |                          D2 PDK-53 WS3-250-Val attenuation locus (wt. D2 16681: Glu, nt-5270-G)      5310      5320      5330      5340      5350      5360      5370      5380      5390      400 GTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTTAGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGT  C  H  A  T  F  T  M  R  L  L  S  P  V  R  V  P  N  Y  N  L  I  I  M  D  E  A  H  F  T  D  P  A  S       5410      5420      5430      5440      5450      5460      5470      5480      5490      5500 ATAGGAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTTATGACAGCCACTCCCCCGGGAAGGAGAGACCCATTTCCTC I  A  A  R  G  Y  I  S  T  R  V  E  M  G  E  A  A  G  I  F  M  T  A  T  P  P  G  S  R  D  P  F  P  Q       5510      5520      5530      5540      5550      5560      5570      5580      5590     5600 AGAGCAATGCACCAATCATAGATGAAGAAAGAGAAATCCCTGAACGCTCGTGGAATTCCGGACATGAATGGGTCACGGATTTTAAAGGGAAGACTGTTTG   S  N  A  P  I  I  D  E  E  R  E  I  P  E  R  S  W  N  S  G  H  E  W  V  T  D  F  K  G  K  T  V  W                                               |                                    D2 PDK-53 silent mutation nt-5547-C (wt. D2 16681: T)       5610      5620      5630      5640      5650      5660      5670      5680      5690      5700 GTTCGTTCCAAGTATAAAAGGAGGAAATGATATAGGAGCTTGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAG  F  V  P  S  I  K  A  G  N  D  I  A  A  C  L  R  K  N  G  K  K  V  I  Q  L  S  R  K  T  F  D  S  E       5710      5720      5730      5740      5750      5760      5770      5780      5790      5800 TATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATGGGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGAC Y  V  K  T  R  T  N  D  W  D  F  V  V  T  T  D  I  S  E  M  G  A  N  F  K  A  E  R  V  I  D  P  R  R       5810      5820      5830      5840      5850      5860      5870      5880      5890      5900 GCTGCATGAAACCAGTCATACTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAG   C  M  K  P  V  I  L  T  D  G  E  E  R  V  I  L  A  G  P  M  P  V  T  H  S  S  A  A  Q  R  R  G  R       5910      5920      5930      5940      5950      5960      5970      5980      5990      6000 AATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATG  I  G  R  N  P  K  N  E  N  D  Q  Y  I  Y  M  G  E  P  L  E  N  D  E  D  C  A  H  W  K  E  A  K  M       6010      6020      6030      6040      6050      6060      6070      6080      6090      6100 CTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGTGAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAG L  L  D  N  I  N  T  P  E  G  I  I  P  S  M  F  E  P  E  R  E  K  V  D  A  I  D  G  E  Y  R  L  R  G       6110      6120      6130      6140      6150      6160      6170      6180      6190      6200 GAGAAGCAAGGAAAACCTTTGTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAAGGCATCAACTACGCAGACAG   E  A  R  K  T  F  V  D  L  M  R  R  G  D  L  P  V  W  L  A  Y  R  V  A  A  E  G  I  N  Y  A  D  R       6210      6220      6230      6240      6250      6260      6270      6280      6290      6300 AAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTAGAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCC  R  W  C  F  D  G  V  K  N  N  Q  I  L  E  E  N  V  E  V  E  I  W  T  K  E  G  E  R  K  K  L  K  P                                                                            >NS4A       6310      6320      6330      6340      6350      6360      6370      6380      6390      6400 AGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTTGCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAG R  W  L  D  A  R  I  Y  S  D  P  L  A  L  K  E  F  K  E  F  A  A  G  R  K  S  L  T  L  N  L  I  T  E       6410      6420      6430      6440      6450      6460      6470      6480      6490      6500 AAATGGGTAGGCTCCCAACCTTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAGGCAGGTGGAAGGGCGTACAA   M  G  R  L  P  T  F  M  T  Q  K  A  R  D  A  L  D  N  L  A  V  L  H  T  A  E  A  G  G  R  A  Y  N       6510      6520      6530      6540      6550      6560      6570      6580      6590      6600 CCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGCA  H  A  L  S  E  L  P  E  T  L  E  T  L  L  L  L  T  L  L  A  T  V  T  G  G  I  F  L  F  L  M  S  A                                                                                                  |                                       D2 PDK-53 specific NS4A-75-Ala (wt. D2 16681: Gly, nt-6599-G)       6610      6620      6630      6640      6650      6660      6670      6680      6690      6700 AGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTATGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAA R  G  I  G  K  M  T  L  G  M  C  C  I  I  T  A  S  I  L  L  W  Y  A  Q  I  Q  P  H  W  I  A  A  S  I       6710      6720      6730      6740      6750      6760      6770      6780      6790      6800 TAATACTGGAGTTTTTTCTCATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACCTACGTTGTCATAGCCATCCT   I  L  E  F  F  L  I  V  L  L  I  P  E  P  E  K  Q  R  T  P  Q  D  N  Q  L  T  Y  V  V  I  A  I  L                          >NS4B       6810      6820      6830      6840      6850      6860      6870      6880      6890      6900 CACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGC  T  V  V  A  A  T  M  A  N  E  M  G  F  L  E  K  T  K  K  D  L  G  L  G  S  I  A  T  Q  Q  P  E  S       6910      6920      6930      6940      6950      6960      6970      6980      6990      7000 AACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATT N  I  L  D  I  D  L  R  P  A  S  A  W  T  L  Y  A  V  A  T  T  F  V  T  P  M  L  R  H  S  I  E  N  S       7010      7020      7030      7040      7050      7060      7070     7080      7090      7100 CCTCAGTGAATGTGTCCCTAACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCC   S  V  N  V  S  L  T  A  I  A  N  Q  A  T  V  L  M  G  L  G  K  G  W  P  L  S  K  M  D  I  G  V  P       7110      7120      7130      7140      7150      7160      7170      7180      7190      7200 CCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACTCTCACAGGAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTC  L  L  A  I  G  C  Y  S  Q  V  N  P  I  T  L  T  A  A  L  F  L  L  V  A  H  Y  A  I  I  G  P  G  L       7210      7220      7230      7240      7250      7260      7270      7280      7290      7300 CAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGGAGCGGCGGGCATCATGAAAAACCCAACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATAC Q  A  K  A  T  R  E  A  Q  K  R  A  A  A  G  I  M  K  N  P  T  V  D  G  I  T  V  I  D  L  D  P  I  P       7310      7320      7330      7340      7350      7360      7370      7380      7390      7400 CTTATGATCCGAAGTTTGAAAAGGAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGGACTACATGGGCTCTGTGTGA   Y  D  P  K  F  E  K  Q  L  G  Q  V  M  L  L  V  L  C  V  T  Q  V  L  M  M  R  T  T  W  A  L  C  E  |Additional silent mutation (nt-7311 A-to-G, in master and pre-master seed)       7410      7420      7430      7440      7450      7460      7470      7480      7490      7500 GGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTT  A  L  T  L  A  T  G  P  I  S  T  L  W  E  G  N  P  G  R  F  W  N  T  T  I  A  V  S  M  A  N  I  F                                                                      >NS5       7510      7520      7530      7540      7550      7560      7570      7580      7590      7600 AGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAACACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAG R  G  S  Y  L  A  G  A  G  L  L  F  S  I  M  K  N  T  T  N  T  R  R  G  T  G  N  I  G  E  T  L  G  E       7610      7620      7630      7640      7650      7660      7670      7680      7690      7700 AGAAATGGAAAAGCCGATTGAACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGATAGAACCTTAGCAAAAGAAGG   K  W  K  S  R  L  N  A  L  G  K  S  E  F  Q  I  Y  K  K  S  G  I  Q  E  V  D  R  T  L  A  K  E  G       7710      7720      7730      7740      7750      7760      7770      7780      7790      7800 CATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTA  I  K  R  G  E  T  D  H  H  A  V  S  R  G  S  A  K  L  R  W  F  V  E  R  N  M  V  T  P  E  G  K  V       7810      7820      7830      7840      7850      7860      7870      7880      7890      7900 GTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACG V  D  L  G  C  G  R  G  G  W  S  Y  Y  C  G  G  L  K  N  V  R  E  V  K  G  L  T  K  G  G  P  G  H  E       7910      7920      7930      7940      7950      7960      7970      7980      7990      8000 AAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCAGAAAAGTGTGACACATTATT   E  P  I  P  M  S  T  Y  G  W  N  L  V  R  L  Q  S  G  V  D  V  F  F  I  P  P  E  K  C  D  T  L  L       8010      8020      8030      8040      8050      8060      8070      8080      8090      8100 GTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAAGCAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAA  C  D  I  G  E  S  S  P  N  P  T  V  E  A  G  R  T  A  R  V  L  N  A  V  E  N  W  L  N  N  N  T  Q       8110      8120      8130      8140      8150      8160      8170      8180      8190      8200 TTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCT F  C  I  K  V  L  N  P  Y  M  P  S  V  T  E  K  M  E  A  L  Q  R  K  Y  G  G  A  L  V  R  N  P  L  S       8210      8220      8230      8240      8250      8260      8270      8280      8290      8300 CACGAAACTCCACACATGAGATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATCAACAGATTTAC   R  N  S  T  H  E  M  Y  W  V  S  N  A  S  G  N  I  V  S  S  V  N  M  I  S  R  M  L  I  N  R  F  T       8310      8320      8330      8340      8350      8360      8370      8380      8390      8400 AATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGACCTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATT  M  R  Y  K  K  A  T  Y  E  P  D  V  D  L  G  S  G  T  R  N  I  G  I  E  S  E  I  P  N  L  D  I  I       8410      8420      8430      8440      8450      8460      8470      8480      8490      8500 GGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGACCACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAA G  K  R  I  E  K  I  K  Q  E  H  E  T  S  W  H  Y  D  Q  D  H  P  Y  K  T  W  A  Y  H  G  S  Y  E  T       8510      8520      8530      8540      8550      8560      8570      8580      8590      8600 CAAAACAGACTGGATCAGCATCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATGGTGACACAGATGGCAATGAC   K  Q  T  G  S  A  S  S  M  V  N  G  V  V  R  L  L  T  K  P  W  D  V  V  P  M  V  T  Q  M  A  M  T       8610      8620      8630      8640      8650      8660      8670      8680      8690      8700 AGACACGACTCCATTTGGACAACAGCGCGTTTTTAAAGAGAAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACA  D  T  T  P  F  G  Q  Q  R  V  F  K  E  K  V  D  T  R  T  Q  E  P  K  E  G  T  K  K  L  M  K  I  T       8710      8720      8730      8740      8750      8760      8770      8780      8790      8800 GCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAAGAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGG A  E  W  L  W  K  E  L  G  K  K  K  T  P  R  M  C  T  R  E  E  F  T  R  K  V  R  S  N  A  A  L  G  A       8810      8820      8830      8840      8850      8860      8870      8880      8890      8900 CCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGA   I  F  T  D  E  N  K  W  K  S  A  R  E  A  V  E  D  S  R  F  W  E  L  V  D  K  E  R  N  L  H  L  E       8910      8920      8930      8940      8950      8960      8970      8980      8990      9000 AGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGCAGAGCCATATGGTACATG  G  K  C  E  T  C  V  Y  N  M  M  G  K  R  E  K  K  L  G  E  F  G  K  A  K  G  S  R  A  I  W  Y  M       9010      9020      9030      9040      9050      9060      9070      9080      9090      9100 TGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAG W  L  G  A  R  F  L  E  F  E  A  L  G  F  L  N  E  D  H  W  F  S  R  E  N  S  L  S  G  V  E  G  E  G       9110     9120      9130      9140      9150      9160      9170      9180      9190      9200 GGCTGCACAAGCTAGGTTACATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGATGGGATACAAGAATCACACT   L  H  K  L  G  Y  I  L  R  D  V  S  K  K  E  G  G  A  M  Y  A  D  D  T  A  G  W  D  T  R  I  T  L       9210      9220      9230      9240      9250      9260      9270      9280      9290      9300 AGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATGGAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTG  E  D  L  K  N  E  E  M  V  T  N  H  M  E  G  E  H  K  K  L  A  E  A  I  F  K  L  T  Y  Q  N  K  V       9310      9320      9330      9340      9350      9360      9370      9380      9390      9400 GTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATA V  R  V  Q  R  P  T  P  R  G  T  V  M  D  I  I  S  R  R  D  Q  R  G  S  G  Q  V  G  T  Y  G  L  N  T       9410      9420      9430      9440      9450      9460      9470      9480      9490      9500 CTTTCACCAATATGGAAGCCCAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATCACAGAAGAAATCGCTGTGCA   F  T  N  M  E  A  Q  L  I  R  Q  M  E  G  E  G  V  F  K  S  T  Q  H  L  T  I  T  E  E  I  A  V  Q       9510      9520      9530      9540      9550      9560      9570      9580      9590      9600 AAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCT  N  W  L  A  R  V  G  R  E  R  L  S  R  M  A  I  S  G  D  D  C  V  V  K  P  L  D  D  R  F  A  S  A       9610      9620      9630      9640      9650      9660      9670      9680      9690      9700 TTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCAAGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCAC L  T  A  L  N  D  M  G  K  I  R  K  D  I  Q  Q  W  E  P  S  R  G  W  N  D  W  T  Q  V  P  F  C  S  H       9710      9720      9730      9740      9750      9760      9770      9780      9790      9800 ACCATTTCCATGAGTTAATCATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGAGCCCGAATCTCCCAAGGAGC   H  F  H  E  L  I  M  K  D  G  R  V  L  V  V  P  C  R  N  Q  D  E  L  I  G  R  A  R  I  S  Q  G  A       9810      9820      9830      9840      9850      9860      9870      9880      9890      9900 AGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAAT  G  W  S  L  R  E  T  A  C  L  G  K  S  Y  A  Q  M  W  S  L  M  Y  F  H  R  R  D  A  R  A  A  A  N       9910      9920      9930      9940      9950      9960      9970      9980      9990     10000 GCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATACATGCTAAACATGAATGGATGACAACGGAAGACATGCTGA A  I  C  S  A  V  P  S  H  W  V  P  T  S  R  T  T  W  S  I  H  A  K  H  E  W  M  T  T  E  D  M  L  T      10010     10020     10030     10040     10050     10060     10070     10080     10090     10100 CAGTCTGGAACAGGGTGTGGATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACTTGGGGAAAAGAGAAGA   V  W  N  R  V  W  I  Q  E  N  P  W  M  E  D  K  T  P  V  E  S  W  E  E  I  P  Y  L  G  K  R  E  D      10110     10120     10130     10140     10150     10160     10170     10180     10190     10200 CCAATGGTGCGGCTCATTGATTGGGTTAACAAGGAGGGCCACCTGGGCAAAGAACATCCAAGGAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAA  Q  W  C  G  S  L  I  G  L  T  S  R  A  T  W  A  K  N  T  Q  A  A  I  N  Q  V  R  S  L  I  G  N  E                                                                         >3′-Noncoding Region      10210     10220     10230     10240     10250     10260     10270     10280     10290     10300 GAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGGAGGAGTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTA E  Y  T  D  Y  M  P  S  M  K  R  F  R  R  E  E  E  E  A  G  V  L  W  *      10310     10320     10330     10340     10350     10360     10370     10380     10390     10400 GAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCATAAATGCCATAG      10410     10420     10430     10440     10450     10460     10470     10480     10490     10500 CTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGC      10510     10520     10530     10540     10550     10560     10570     10580     10590     10600 GGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGAAGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGAC      10610     10620     10630     10640     10650     10660     10670     10680     10690     10700 CCCCCCGAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATG      10710     10720  GTGCTGTTGAATCAACAGGTTCT 

DENvax-2 Master Virus Seed (MVS)

Nucleotide sequence of the recombinant viral genome and deduced aminoacid sequence of the translated protein are provided herein. Theengineered virus is based on D2 PDK-53 virus. All engineeredsubstitutions that are different from wild-type DEN-2 16681 virus (alsothe parental virus for PDK-53), as well as extra mutations (changes fromengineered cDNA clone) detected in the MVS are marked.

Substitutions Included in the Genome and Protein:

D2 PDK-53 virus backbone (change from wt D2 16681): all in bold

-   -   a. 5′-noncoding region (NCR)-57 (nt-57 C-to-T): major        attenuation locus (in red)    -   b. prM-29 Asp-to-Val (nt-524 A-to-T)    -   c. nt-2055 C-to-T (E gene) silent mutation    -   d. NS1-53 Gly-to-Asp (nt-2579 G-to-A): major attenuation locus        (in red)    -   e. NS2A-181 Leu-to-Phe (nt-4018 C-to-T)    -   f. NS3-250 Glu-to-Val (nt-5270 A-to-T): major attenuation locus        (in red)    -   g. nt-5547 (NS3 gene) T-to-C silent mutation    -   h. NS4A-75 Gly-to-Ala (nt-6599 G-to-C)    -   * nt-8571 C-to-T silent mutation of PDK-53 is not engineered in        the vaccine virus

Engineered clone marker (silent mutation):

-   -   a. nt-900 T-to-C silent mutation: infectious clone marker

Additional substitutions found in vaccine seed (0.02% nt different fromoriginal clone)

-   -   a. prM-52 Lys-to-Glu (nt-592 A-to-G), in bold    -   b. NS5-412 Ile-to-Val (nt-8803 A-to-G), in bold

                                      NCR-57-T. D2 PDK-53 attenuation locus (wt D2 16681: C) >5′-NC                                                                                               >C         10        20        30        40        50        60        70        80        90       100       110       120 AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAATGTAGTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGAATAACCAACGGAAAAAGGCG                                                                                                 M  N  N  Q  R  K  K  A        130       140       150       160       170       180       190       200       210       220       230       240 AAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACTTGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATG K  N  T  P  F  N  M  L  K  R  E  R  N  A  V  S  T  V  Q  Q  L  T  K  R  F  S  L  G  M  L  Q  G  R  G  P  L  K  L  F  M        250       260       270      280       290       300       310       320       330       340       350       360 GCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATATTGAAGAGATGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATT A  L  V  A  F  L  R  F  L  T  I  P  P  T  A  G  I  L  K  R  W  G  T  I  K  K  S  K  A  I  N  V  L  R  G  F  R  K  E  I                                                                               >prM        370       380       390       400       410       420       430       440       450       460       470       480 GGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTGCAGGCATGATCATTATGCTGATTCCAACAGTGATGGCGTTCCATTTAACCACACGTAACGGAGAACCACACATGATCGTC G  R  M  L  N  I  L  N  A  R  R  R  S  A  G  M  I  I  M  L  I  P  T  V  M  A  F  H  L  T  T  R  N  G  E  P  H  M  I  V        490       500       510       520       530       540       550       560       570       580       590       600 AGCAGACAAGAGAAAGGGAAAAGTCTTCTGTTTAAAACAGAGGTTGGCGTGAACATGTGTACCCTCATGGCCATGGACCTTGGTGAATTGTGTGAAGACACAATCACGTACGAGTGTCCC S  R  Q  E  K  G  K  S  L  L  F  K  T  E  V  G  V  N  M  C  T  L  M  A  M  D  L  G  E  L  C  E  D  T  I  T  Y  E  C  P                                           |                                                                   |D2 PDK-53 specific prM-29 Val (wt D2 16681 Asp, nt-524-A)    Additional prM-52 Lys-to-Glu mutation (nt-592 A-to-G)  >M        610       620       630       640       650       660       670       680       690       700       710       720 CTTCTCAGGCAGAATGAGCCAGAAGACATAGACTGTTGGTGCAACTCTACGTCCACGTGGGTAACTTATGGGACGTGTACCACCATGGGAGAACATAGAAGAGAAAAAAGATCAGTGGCA L  L  R  Q  N  E  P  E  D  I  D  C  W  C  N  S  T  S  T  W  V  T  Y  G  T  C  T  T  M  G  E  H  R  R  E  K  R  S  V  A        730       740       750       760       770       780       790       800       810       820       830       840 CTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGTCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTCACC L  V  P  H  V  G  M  G  L  E  T  R  T  E  T  W  M  S  S  E  G  A  W  K  H  V  Q  R  I  E  T  W  I  L  R  H  P  G  F  T  >E        850       860       870       880       890       900       910       920       930       940       950       960 ATGATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATCTTCATCTTACTGACAGCTGICACTCCTTCAATGACAATGCGTTGCATAGGAATGICAAAT M  M  A  A  I  L  A  Y  T  I  G  T  T  H  F  Q  R  A  L  I  F  I  L  L  T  A  V  T  P  S  M  T  M  R  C  I  G  M  S  N                                                            |                                               Engineered silent clone marker: nt-900 T-to-C silent mutation        970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080 AGAGACTTTGTGGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGAAGCTGTGTGACGACGATGGCAAAAAACAAACCAACATTGGATTTTGAACTGATAAAAACA R  D  F  V  E  G  V  S  G  G  S  W  V  D  I  V  L  E  H  G  S  C  V  T  T  M  A  K  N  K  P  T  L  D  F  E  L  I  K  T       1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200 GAAGCCAAACAGCCTGCCACCCTAAGGAAGTACTGTATAGAGGCAAAGCTAACCAACACAACAACAGAATCTCGCTGCCCAACACAAGGGGAACCCAGCCTAAATGAAGAGCAGGACAAA E  A  K  Q  P  A  T  L  R  K  Y  C  I  E  A  K  L  T  N  T  T  T  E  S  R  C  P  T  Q  G  E  P  S  L  N  E  E  Q  D  K       1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320 AGGTTCGTCTGCAAACACTCCATGGTAGACAGAGGATGGGGAAATGGATGTGGACTATTTGGAAAGGGAGGCATTGTGACCTGTGCTATGTTCAGATGCAAAAAGAACATGGAAGGAAAA R  F  V  C  K  H  S  M  V  D  R  G  W  G  N  G  C  G  L  F  G  K  G  G  I  V  T  C  A  M  F  A  C  K  K  N  M  E  G  K       1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440 GTTGTGCAACCAGAAAACTTGGAATACACCATTGTGATAACACCTCACTCAGGGGAAGAGCATGCAGTCGGAAATGACACAGGAAAACATGGCAAGGAAATCAAAATAACACCACAGAGT V  V  Q  P  E  N  L  E  Y  T  I  V  I  T  P  H  S  G  E  E  H  A  V  G  N  D  T  G  K  H  G  K  E  I  K  I  T  P  Q  S       1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560 TCCATCACAGAAGCAGAATTGACAGGTTATGGCACTGTCACAATGGAGTGCTCTCCAAGAACGGGCCTCGACTTCAATGAGATGGTGTTGCTGCAGATGGAAAATAAAGCTIGGCTGGTG S  I  T  E  A  E  L  T  G  Y  G  T  V  T  M  E  C  S  P  R  T  G  L  D  F  N  E  M  V  L  L  Q  M  E  N  K  A  W  L  V       1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680 CACAGGCAATGGTTCCTAGACCTGCCGTTACCATGGTTGCCCGGAGCGGACACACAAGGGTCAAATTGGATACAGAAAGAGACATTGGTCACTTTCAAAAATCCCCATGCGAAGAAACAG H  R  Q  W  F  L  D  L  P  L  P  W  L  P  G  A  D  T  Q  G  S  N  W  I  Q  K  E  T  L  V  T  F  K  N  P  H  A  K  K  Q       1690      1700      1710      1720      1730      1740      1750      1760      1770      1780      1790      1800 GATGTTGTTGTTTTAGGATCCCAAGAAGGGGCCATGCACACAGCACTTACAGGGGCCACAGAAATCCAAATGTCATCAGGAAACTTACTCTTCACAGGACATCTCAAGTGCAGGCTGAGA D  V  V  V  L  G  S  Q  E  G  A  M  H  T  A  L  T  G  A  T  E  I  Q  M  S  S  G  N  L  L  F  T  G  H  L  K  C  A  L  R       1810      1820      1830      1840      1850      1860      1870      1880      1890      1900      1910      1920 ATGGACAAGCTACAGCTCAAAGGAATGTCATACTCTATGTGCACAGGAAAGTTTAAAGTTGTGAAGGAAATAGCAGAAACACAACATGGAACAATAGTTATCAGAGTGCAATATGAAGGG M  D  K  L  Q  L  K  G  M  S  Y  S  M  C  T  G  K  F  K  V  V  K  E  I  A  E  T  Q  H  G  T  I  V  I  R  V  Q  Y  E  G       1930      1940      1950      1960      1970      1980      1990      2000      2010      2020      2030      2040 GACGGCTCTCCATGCAAGATCCCTTTTGAGATAATGGATTTGGAAAAAAGACATGTCTTAGGTCGCCTGATTACAGTCAACCCAATTGTGACAGAAAAAGATAGCCCAGTCAACATAGAA D  G  S  P  C  K  I  P  F  E  I  M  D  L  E  K  R  H  V  L  G  R  L  I  T  V  N  P  I  V  T  E  K  D  S  P  V  N  I  E       2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160 GCAGAACCTCCATTTGGAGACAGCTACATCATCATAGGAGTAGAGCCGGGACAACTGAAGCTCAACTGGTTTAAGAAAGGAAGTTCTATCGGCCAAATGTTTGAGACAACAATGAGGGGG A  E  P  P  F  G  D  S  Y  I  I  I  G  V  E  P  G  Q  L  K  L  N  W  F  K  K  G  S  S  I  G  Q  M  F  E  T  T  M  R  G               | D2 PDK-53 nt-2055-T silent mutation (D2 16681: C)       2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280 GCGAAGAGAATGGCCATTTTAGGTGACACAGCCTGGGATTTTGGATCCTTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTCTTTGGAGCAATCTATGGAGCTGCCTTC A  K  R  M  A  I  L  G  D  T  A  W  D  F  G  S  L  G  G  V  F  T  S  I  G  K  A  L  H  Q  V  F  G  A  I  Y  G  A  A  F       2290      2300      2310 2320      2330      2340      2350      2360      2370      2380      2390      2400 AGTGGGGTTTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTGTCTGTGACACTAGTATTGGTGGGAATTGTGACACTGTAT S  G  V  S  W  T  M  K  I  L  I  G  V  I  I  T  W  I  G  M  N  S  R  S  T  S  L  S  V  T  L  V  L  V  G  I  V  T  L                      >NS1       2410      2420      2430      2440      2450      2460      2470      2480      2490      2500      2510      2520 TTGGGAGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGGACAGAACAATACAAG L  G  V  M  V  Q  A  D  S  G  C  V  V  S  W  K  N  K  E  L  K  C  G  S  G  I  F  I  T  D  N  V  H  T  W  T  E  Q  Y  K       2530      2540      2550      2560      2570      2580      2590      2600      2610      2620      2630      2640 TTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGACATTTGTGGAATCCGCTCAGTAACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCA F  Q  P  E  S  P  S  K  L  A  S  A  I  Q  K  A  H  E  E  D  I  C  G  I  R  S  V  T  R  L  E  N  L  M  W  K  Q  I  T  P                                                           |                                                D2 PDK-53 NSa-53-Asp attenuation locus (wt. D2 16681: Gly, nt-2579-G)      2650      2660      2670      2680      2690      2700      2710      2720      2730      2740      2750      2760 GAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATCAAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTAT E  L  N  H  I  L  S  E  N  E  V  K  L  T  I  M  T  G  D  I  K  G  I  M  Q  A  G  K  R  S  L  R  P  Q  P  T  E  L  K  Y       2770      2780      2790      2800      2810      2820      2830      2840      2850      2860      2870      2880 TCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAGAGTCTCATAACCAGACCTTTCTCATTGATGGCCCCGAAACAGCAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTG S  W  K  T  W  G  K  A  K  M  L  S  T  E  S  H  N  Q  T  F  L  I  D  G  P  E  T  A  E  C  P  N  T  N  R  A  W  N  S  L       2890      2900      2910      2920      2930      2940      2950      2960      2970      2980      2990      3000 GAAGTTGAAGACTATGGCTTTGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAAAAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCC E  V  E  D  Y  G  F  G  V  F  T  T  N  I  W  L  K  L  K  E  K  Q  D  V  F  C  D  S  K  L  M  S  A  A  I  K  D  N  R  A       3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120 GTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAAAATCACACACCCTCTGGAGC V  H  A  D  M  G  Y  W  I  E  S  A  L  N  D  T  W  K  I  E  K  A  S  F  I  E  V  K  N  C  H  W  P  K  S  H  T  L  W  S       3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240 AATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAACACAACTATAGACCAGGCTACCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTT N  G  V  L  E  S  E  M  I  I  P  K  N  L  A  G  P  V  S  Q  H  N  Y  R  P  G  Y  H  T  Q  I  T  G  P  W  H  L  G  K  L       3250      3260      3270      3280      3290      3300      3310      3320      3330      3340      3350      3360 GAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAATAGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGC E  M  D  F  D  F  C  D  G  T  T  V  V  V  T  E  D  C  G  N  R  G  P  S  L  A  T  T  T  A  S  G  K  L  I  T  E  W  C  C                                                                                                                     >NS2A       3370      3380      3390      3400      3410      3420      3430      3440      3450      3460      3470      3480 CGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGGTGCTGGTACGGGATGGAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGA R  S  C  T  L  P  P  L  R  Y  R  G  E  D  G  C  W  Y  G  M  E  I  R  P  L  K  E  K  E  E  N  L  V  N  S  L  V  T  A  G       3490      3500      3510      3520      3530      3540      3550      3560      3570      3580      3590      3600 CATGGGCAGGTCGACAACTTTTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAAATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTG H  G  Q  V  D  N  F  S  L  G  V  L  G  M  A  L  F  L  E  E  M  L  R  T  R  V  G  T  K  H  A  I  L  L  V  A  V  S  F  V       3610      3620      3630      3640      3650      3660      3670      3680      3690      3700      3710      3720 ACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGCGCCACTATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCCTACTAGCAGCCTTC T  L  I  T  G  N  M  S  F  R  D  L  G  R  V  M  V  M  V  G  A  T  M  T  D  D  I  G  M  G  V  T  Y  L  A  L  L  A  A  F       3730      3740      3750      3760      3770      3780      3790      3800      3810      3820      3830      3840 AAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTGATGATGACTACTATAGGAATTGTACTCCTCTCCCAGAGCACCATACCAGAGACCATTCTT K  V  R  P  T  F  A  A  G  L  L  L  R  K  L  T  S  K  E  L  M  M  T  T  I  G  I  V  L  L  S  Q  S  T  I  P  E  T  I  L       3850      3860      3870      3880      3890      3900      3910      3920      3930      3940      3950      3960 GAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAAAAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTA E  L  T  D  A  L  A  L  G  M  M  V  L  K  M  V  R  N  M  E  K  Y  Q  L  A  V  T  I  M  A  I  L  C  V  P  N  A  V  I  L       3970      3980      3990      4000      4010      402     0 4030     4040      4050      4060      4070      4080 CAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCCGTTTCCCCACTGTTCTTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTC Q  N  A  W  K  V  S  C  T  I  L  A  V  V  S  V  S  P  L  F  L  T  S  S  Q  Q  K  T  D  W  I  P  L  A  L  T  I  K  G  L                                                          |                                                    D2 PDK-53 specific NS2A-181-Phe (wt D2 16681: Leu, nt-4018-C)                                                    >NS2B       4090      4100      4110      4120      4130      4140      4150      4160      4170      4180      4190      4200 AATCCAACAGCTATTTTTCTAACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCATTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAA N  P  T  A  I  F  L  T  T  L  S  R  T  S  K  K  R  S  W  P  L  N  E  A  I  M  A  V  G  M  V  S  I  L  A  S  S  L  L  K       4210      4220      4230      4240      4250      4260      4270      4280      4290      4300      4310      4320 AATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAGCCGATGTCAAATGGGAAGAC N  D  I  P  M  T  G  P  L  V  A  G  G  L  L  T  V  C  Y  V  L  T  G  R  S  A  D  L  E  L  E  R  A  A  D  V  K  W  E  D       4330      4340      4350      4360      4370      4380      4390      4400      4410      4420      4430      4440 CAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAATGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTG Q  A  E  I  S  G  S  S  P  I  L  S  I  T  I  S  E  D  G  S  M  S  I  K  N  E  E  E  E  Q  T  L  T  I  L  I  R  T  G  L                                                                                  >NS3       4450      4460      4470      4480      4490      4500      4510      4520      4530      4540      4550      4560 CTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATG L  V  I  S  G  L  F  P  V  S  I  P  I  T  A  A  A  W  Y  L  W  E  V  K  K  Q  R  A  G  V  L  W  D  V  P  S  P  P  P  M       4570      4580      4590      4600      4610      4620      4630      4640      4650      4660      4670      4680 GGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGCAAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACA G  K  A  E  L  E  D  G  A  Y  R  I  K  Q  K  G  I  L  G  Y  S  Q  I  G  A  G  V  Y  K  E  G  T  F  H  T  M  W  H  V  T       4690      4700      4710      4720      4730      4740      4750      4760      4770      4780      4790      4800 CGTGGCGCTGTTCTAATGCATAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAA R  G  A  V  L  M  H  K  G  K  R  I  E  P  S  W  A  D  V  K  K  D  L  I  S  Y  G  G  G  W  K  L  E  G  E  W  K  E  G  E       4810      4820      4830      4840      4850      4860      4870      4880      4890      4900      4910      4920 GAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCTGGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTATCTCTGGACTTTTCTCCTGGA E  V  Q  V  L  A  L  E  P  G  K  N  P  R  A  V  Q  T  K  P  G  L  F  K  T  N  A  G  T  I  G  A  V  S  L  D  F  S  P  G         4930      4940      4950      4960      4970      4980      4990      5000      5010      5020      5030      5040 ACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGTGTTGTTACAAGGAGTGGAGCATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAA T  S  G  S  P  I  I  D  K  K  G  K  V  V  G  L  Y  G  N  G  V  V  T  R  S  G  A  Y  V  S  A  I  A  Q  T  E  K  S  I  E       5050      5060      5070      5080      5090      5100      5110      5120      5130      5140      5150      5160 GACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTCCACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAA D  N  P  E  I  E  D  D  I  F  R  K  R  A  L  T  I  M  D  L  H  P  G  A  G  K  T  K  R  Y  L  P  A  I  V  R  E  A  I  K       5170      5180      5190      5200      5210      5220      5230      5240      5250      5260      5270      5280 CGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTGTGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGTGCACACCGGG R  G  L  R  T  L  I  L  A  P  T  R  V  V  A  A  E  M  E  E  A  L  R  G  L  P  I  R  Y  Q  T  P  A  I  R  A  V  H  T  G                                                                                                  |                                             D2 PDK-53 WS3-250-Val attenuation locus (wt D2 16681: Glu, nt-5270-A)      5290      5300      5310      5320      5330      5340      5350      5360      5370      5380      5390      5400 CGGGAGATTGTGGACCTAATGTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTTAGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGT R  E  I  V  D  L  M  C  H  A  T  F  T  M  R  L  L  S  P  V  R  V  P  N  Y  N  L  I  I  M  D  E  A  H  F  T  D  P  A  S       5410      5420      5430      5440      5450      5460      5470      5480      5490      5500      5510      5520 ATAGCAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTTATGACAGCCACTCCCCCGGGAAGCAGAGACCCATTTCCTCAGAGCAATGCACCAATCATA I  A  A  R  G  Y  I  S  T  R  V  E  M  G  E  A  A  G  I  F  M  T  A  T  P  P  G  S  R  D  P  F  P  Q  S  N  A  P  I  I       5530      5540      5550      5560      5570      5580      5590      5600      5610      5620      5630      5640 GATGAAGAAAGAGAAATCCCTGAACGCTCGTGGAATTCCGGACATGAATGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTCGTTCCAAGTATAAAAGCAGGAAATGATATAGCAGCT D  E  E  R  E  I  P  E  R  S  W  N  S  G  H  E  W  V  T  D  F  K  G  K  T  V  W  F  V  P  S  I  K  A  G  N  D  I  A  A                                    |                                 D2 PDK-53 silent mutation nt-5547-C (D2 16681: T)       5650      5660      5670      5680      5690      5700      5710      5720      5730      5740      5750      5760 TGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAGTATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATG C  L  R  K  N  G  K  K  V  I  Q  L  S  R  K  T  F  D  S  E  Y  V  K  T  R  I  N  D  W  D  F  V  V  I  T  D  I  S  E  M       5770      5780      5790      5800      5810      5820      5830      5840      5850      5860      5870      5880 GGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGACGCTGCATGAAACCAGTCATACTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGT G  A  N  F  K  A  E  R  V  I  D  P  R  A  C  M  K  P  V  I  L  T  D  G  E  E  R  V  I  L  A  G  P  M  P  V  T  H  S  S       5890      5900      5910      5920      5930      5940      5950      5960      5970      5980      5990      6000 GCAGCACAAAGAAGAGGGAGAATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATG A  A  Q  R  R  G  R  I  G  R  N  P  K  N  E  N  D  Q  Y  I  Y  M  G  E  P  L  E  N  D  E  D  C  A  H  W  K  E  A  K  M       6010      6020      6030      6040      6050      6060      6070      6080      6090      6100      6110      6120 CTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGTGAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAGGAGAAGCAAGGAAAACCTTT L  L  D  N  I  N  T  P  E  G  I  I  P  S  M  F  E  P  E  R  E  K  V  D  A  I  D  G  E  Y  R  L  R  G  E  A  R  K  T  F       6130      6140      6150      6160      6170      6180      6190      6200      6210      6220      6230      6240 GTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTA V  D  L  M  A  R  G  D  L  P  V  W  L  A  Y  R  V  A  A  E  G  I  N  Y  A  D  R  A  W  C  F  D  G  V  K  N  N  Q  I  L        6250      6260      6270      6280      6290      6300      6310      6320      6330      6340      6350      6360 GAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCCAGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTT E  E  N  V  E  V  E  I  W  T  K  E  G  E  R  K  K  L  K  P  R  W  L  D  A  R  I  Y  S  D  P  L  A  L  K  E  F  K  E  F                >NS4A       6370      6380      6390      6400      6410      6420      6430      6440      6450      6460      6470      6480 GCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAGAAATGGGTAGGCTCCCAACCTTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAG A  A  G  R  K  S  L  T  L  N  L  I  T  E  M  G  R  L  P  T  F  M  T  Q  K  A  R  D  A  L  D  N  L  A  V  L  H  T  A  E       6490      6500      6510      6520      6530      6540      6550      6560      6570      6580      6590      6600 GCAGGTGGAAGGGCGTACAACCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGCA A  G  G  R  A  Y  N  H  A  L  S  E  L  P  E  T  L  E  T  L  L  L  L  T  L  L  A  T  V  T  G  G  I  F  L  F  L  M  S  A          |                                                                 D2 PDK-53 specific NS4A-75-Ala (wt D2 16681: Gly, nt-6599-G)       6610      6620      6630      6640      6650      6660      6670      6680      6690      6700      6710      6720 AGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTATGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAATAATACTGGAGTTTTTTCTC R  G  I  G  K  M  T  L  G  M  C  C  I  I  T  A  S  I  L  L  W  Y  A  Q  I  Q  P  H  W  I  A  A  S  I  I  L  E  F  F  L                                                                                                          >NS4B      6730      6740      6750      6760      6770      6780      6790      6800      6810     6820      6830      6840 ATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACCTACGTTGTCATAGCCATCCTCACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTC I  V  L  L  I  P  E  P  E  K  Q  R  T  P  Q  D  N  Q  L  T  Y  V  V  I  A  I  L  T  V  V  A  A  T  M  A  N  E  M  G  F       6850      6860      6870      6880      6890      6900      6910      6920      6930      6940      6950      6960 CTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACA L  E  K  T  K  K  D  L  G  L  G  S  I  A  T  Q  Q  P  E  S  N  I  L  D  I  D  L  R  P  A  S  A  W  T  L  Y  A  V  A  T       6970      6980      6990      7000      7010      7020      7030      7040      7050      7060      7070      7080 ACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATTCCTCAGTGAATGTGTCCCTAACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGICTCGGGAAAGGATGGCCATTGICA T  F  V  T  P  M  L  R  H  S  I  E  N  S  S  V  N  V  S  L  T  A  I  A  N  Q  A  T  V  L  M  G  L  G  K  G  W  P  L  S       7090      7100      7110      7120      7130      7140      7150      7160      7170      7180      7190      7200 AAGATGGACATCGGAGTTCCCCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACTCTCACAGCAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTC K  M  D  I  G  V  P  L  L  A  I  G  C  Y  S  Q  V  N  P  I  T  L  T  A  A  L  F  L  L  V  A  H  Y  A  I  I  G  P  G  L       7210      7220      7230      7240     7250      7260      7270      7280      7290      7300      7310      7320 CAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGCAGCGGCGGGCATCATGAAAAACCCAACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATACCTTATGATCCAAAGTTTGAA Q  A  K  A  T  R  E  A  Q  K  R  A  A  A  G  I  M  K  N  P  T  V  D  G  I  T  V  I  D  L  D  P  I  P  Y  D  P  K  F  E       7330      7340      7350      7360      7370      7380      7390      7400      7410      7420      7430      7440 AAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGG K  Q  L  G  Q  V  M  L  L  V  L  C  V  T  Q  V  L  M  M  R  T  T  W  A  L  C  E  A  L  T  L  A  T  G  P  I  S  T  L  W       7450      7460      7470      7480      7490      7500      7510      7520      7530      7540      7550      7560 GAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAAC E  G  N  P  G  R  F  W  N  T  T  I  A  V  S  M  A  N  I  F  R  G  S  Y  L  A  G  A  G  L  L  F  S  I  M  K  N  T  T  N          >NS5       7570      7580      7590      7600      7610      7620      7630      7640      7650      7660      7670      7680 ACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTGAACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGAT T  R  R  G  T  G  N  I  G  E  T  L  G  E  K  W  K  S  R  L  N  A  L  G  K  S  E  F  Q  I  Y  K  K  S  G  I  Q  E  V  D       7690      7700      7710      7720      7730      7740      7750      7760      7770      7780      7790      7800 AGAACCTTAGCAAAAGAAGGCATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTA R  T  L  A  K  E  G  I  K  R  G  E  T  D  H  H  A  V  S  R  G  S  A  K  L  R  W  F  V  E  R  N  M  V  T  P  E  G  K  V       7810      7820      7830      7840      7850      7860      7870      7880      7890      7900      7910      7920 GTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAACCCATCCCCATGTCA V  D  L  G  C  G  R  G  G  W  S  Y  Y  C  G  G  L  K  N  V  R  E  V  K  G  L  T  K  G  G  P  G  H  E  E  P  I  P  M  S       7930      7940      7950      7960      7970      7980      7990      8000      8010      8020      8030      8040 ACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCAGAAAAGTGTGACACATTATTGTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAA T  Y  G  W  N  L  V  R  L  Q  S  G  V  D  V  F  F  I  P  P  E  K  C  D  T  L  L  C  D  I  G  E  S  S  P  N  P  T  V  E       8050      8060      8070      8080      8090      8100      8110      8120      8130      8140      8150      8160 GCAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAATTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTA A  G  R  T  L  R  V  L  N  L  V  E  N  W  L  N  N  N  T  Q  F  C  I  K  V  L  N  P  Y  M  P  S  V  I  E  K  M  E  A  L         8170      8180      8190      8200      8210      8220      8230      8240      8250      8260      8270      8280 CAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCTCACGAAACTCCACACATGAGATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGG Q  R  K  Y  G  G  A  L  V  R  N  P  L  S  R  N  S  T  H  E  M  Y  W  V  S  N  A  S  G  N  I  V  S  S  V  N  M  I  S  R       8290      8300      8310      8320      8330      8340      8350      8360      8370      8380      8390      8400 ATGTTGATCAACAGATTTACAATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGACCTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATT M  L  I  N  R  F  T  M  R  Y  K  K  A  T  Y  E  P  D  V  D  L  G  S  G  T  R  N  I  G  I  E  S  E  I  P  N  L  D  I  I       8410      8420      8430      8440      8450      8460      8470     8480      8490      8500      8510      8520 GGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGACCACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAACAAAACAGACTGGATCAGCA G  K  R  I  E  K  I  K  Q  E  H  E  T  S  W  H  Y  D  Q  D  H  P  Y  K  T  W  A  Y  H  G  S  Y  E  T  K  Q  T  G  S  A       8530      8540      8550      8560      8570      8580      8590      8600      8610      8620      8630      8640 TCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATGGTGACACAGATGGCAATGACAGACACGACTCCATTIGGACAACAGCGCGTTTTTAAAGAG S  S  M  V  N  G  V  V  R  L  L  T  K  P  W  D  V  V  P  M  V  T  Q  M  A  M  T  D  T  T  P  F  G  Q  Q  R  V  F  K  E       8650      8660      8670      8680      8690      8700      8710      8720      8730      8740      8750      8760 AAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACAGCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAA K  V  D  T  R  T  Q  E  P  K  E  G  T  K  K  L  M  K  I  T  A  E  W  L  W  K  E  L  G  K  K  K  T  P  R  M  C  T  R  E       8770      8780      8790      8800      8810      8820      8830      8840      8850      8860      8870      8880 GAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTIGGGGGCCGTATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTIGGGAGCTGGTTGACAAG E  F  T  R  K  V  A  S  N  A  A  L  G  A  V  F  T  D  E  N  K  W  K  S  A  R  E  A  V  E  D  S  R  F  W  E  L  V  D  K                                              |                                  Additional NS5-412 Ile-to-Val (nt-8803 A-to-G) mutation in master and pre-master seed       8890      8900      8910      8920      8930      8940      8950      8960      8970      8980      8990      9000 GAAAGGAATCTCCATCTTGAAGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGCAGAGCCATATGGTACATG E  R  N  L  H  L  E  G  K  C  E  T  C  V  Y  N  M  M  G  K  R  E  K  K  L  G  E  F  G  K  A  K  G  S  R  A  I  W  Y  M       9010      9020      9030      9040      9050      9060      9070      9080      9090      9100      9110      9120 TGGCTIGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGCACAAGCTAGGTTAC W  L  G  A  R  F  L  E  F  E  A  L  G  F  L  N  E  D  H  W  F  S  R  E  N  S  L  S  G  V  E  G  E  G  L  H  K  L  G  Y       9130      9140      9150      9160      9170      9180      9190      9200      9210      9220      9230      9240 ATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGATGGGATACAAGAATCACACTAGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATG I  L  R  D  V  S  K  K  E  G  G  A  M  Y  A  D  D  T  A  G  W  D  T  R  I  T  L  E  D  L  K  N  E  E  M  V  T  N  H  M       9250      9260      9270      9280      9290      9300      9310      9320      9330      9340      9350      9360 GAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTGGTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGAC E  G  E  H  K  K  L  A  E  A  I  F  K  L  T  Y  Q  N  K  V  V  R  V  Q  R  P  T  P  R  G  T  V  M  D  I  I  S  A  R  D       9370      9380      9390     9400      9410      9420      9430      9440      9450      9460      9470      9480 CAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATACTTTCACCAATATGGAAGCCCAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATC Q  R  G  S  G  Q  V  G  T  Y  G  L  N  T  F  T  N  M  E  A  Q  L  I  R  Q  M  E  G  E  G  V  F  K  S  I  Q  H  L  T  I       9490      9500      9510      9520      9530      9540      9550      9560      9570      9580      9590      9600 ACAGAAGAAATCGCTGTGCAAAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCT T  E  E  I  A  V  Q  N  W  L  A  R  V  G  R  E  R  L  S  R  M  A  I  S  G  D  D  C  V  V  K  P  L  D  D  R  F  A  S  A       9610      9620      9630      9640      9650      9660      9670      9680      9690      9700      9710      9720 TTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCAAGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCACACCATTTCCATGAGTTAATC L  T  A  L  N  D  M  G  K  I  R  K  D  I  Q  Q  W  E  P  S  R  G  W  N  D  W  T  Q  V  P  F  C  S  H  H  F  H  E  L  I       9730      9740      9750      9760      9770      9780      9790      9800      9810      9820      9830      9840 ATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGAGCCCGAATCTCCCAAGGAGCAGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCT M  K  D  G  R  V  L  V  V  P  C  R  N  Q  D  E  L  I  G  R  A  R  I  S  Q  G  A  G  W  S  L  R  E  T  A  C  L  G  K  S       9850      9860      9870      9880      9890      9900      9910      9920      9930      9940      9950      9960 TACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAATGCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATA Y  A  Q  M  W  S  L  M  Y  F  H  A  R  D  L  R  L  A  A  N  A  I  C  S  A  V  P  S  H  W  V  P  T  S  R  T  T  W  S  I       9970      9980      9990     10000     10010     10020     10030     10040     10050     10060     10070     10080 CATGCTAAACATGAATGGATGACAACGGAAGACATGCTGACAGTCTGGAACAGGGTGTGGATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCA H  A  K  H  E  W  M  T  T  E  D  M  L  T  V  W  N  R  V  W  I  Q  E  N  P  W  M  E  D  K  T  P  V  E  S  W  E  E  I  P      10090     10100     10110     10120     10130     10140     10150     10160     10170     10180     10190     10200 TACTTGGGGAAAAGAGAAGACCAATGGTGCGGCTCATTGATTGGGTTAACAAGCAGGGCCACCTGGGCAAAGAACATCCAAGCAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAA Y  L  G  K  R  E  D  Q  W  C  G  S  L  I  G  L  T  S  R  A  T  W  A  K  N  I  Q  A  A  I  N  Q  V  R  S  L  I  G  N  E                                                                      >3′-NC      10210     10220     10230     10240     10250     10260     10270     10280     10290     10300     10310     10320 GAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGCAGGAGTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTAGAAGTCAGGICGGATTAAGC E  Y  T  D  Y  M  P  S  M  K  R  F  R  R  E  E  E  E  A  G  V  L  W      10330     10340     10350     10360     10370     10380     10390     10400     10410     10420     10430     10440 CATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCATAAATGCCATAGCTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGG      10450     10460     10470     10480     10490     10500     10510     10520     10530     10540     10550     10560 TGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGA      10570     10580     10590     10600     10610     10620     10630     10640     10650     10660     10670     10680 AGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGACCCCCCCGAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGICTCCTCAGCATCATTCCAGGCACA      10690     10700     10710     10720 GAACGCCAGAAAATGGAATGGTGCTGTTGAATCAACAGGTTCT 

DENvax-3 Master Virus Seed (MVS)

Nucleotide sequence of the chimeric viral genome and deduced amino acidsequence of the translated protein are provided herein. Most of theprM-E gene (nt-457 to -2373, underlined) is wild-type (wt) DEN-3 16562virus-specific; the remaining nucleotide sequence is DEN-2 PDK-53virus-specific. The E protein of DEN-3 virus has two fewer amino acidsthan the E protein of DEN-2. Therefore, nt position starting from NgoMIVis 6 nt less than the original DEN-2 PDK-53 nt position. All engineeredsubstitutions differ from wt virus (DEN-3 16562 or DEN-2 16681), as wellas extra mutations (changes from engineered cDNA clone) are marked.

Substitutions Included in the Genome and Proein:

Junction sites:

-   -   a. MluI (nt 451-456): engineered silent mutation, nt-453 A-to-G    -   b. NgoMIV (nt 2374-2379): engineered mutations, nt-2375/2376        TG-to-CC (resulted in E-480 Val-to-Ala change)

D2 PDK-53 virus backbone (change from wt D2 16681): in bold

-   -   a. 5′-noncoding region(NCR)-57 (nt-57 C-to-T): major attenuation        locus (in red)    -   b. NS1-53 Gly-to-Asp (nt-2573 G-to-A): major attenuation locus        (in red)    -   c. NS2A-181 Leu-to-Phe (nt-4012 C-to-T)    -   d. NS3-250 Glu-to-Val (nt-5264 A-to-T): major attenuation locus        (in red)    -   e. nt-5541 (NS3 gene) T-to-C silent mutation    -   f. NS4A-75 Gly-to-Ala (nt-6593 G-to-C)    -   * nt-8565 C-to-T silent mutation of PDK-53 is not engineered in        the vaccine virus

Engineered mutation in DEN-3 prM-E (change from wt D3 16562)

-   -   a. Engineered nt-552 C-to-T silent mutation: clone marker    -   b. Engineered E-345 His-to-Leu (nt-1970 A-to-T) for efficient        replication in cultures

Additional substitutions found in vaccine seed (0.02% nt different fromoriginal clone)

-   -   a. E-223 Thr-to-Ser mutation (nt-1603 A-to-T, in bold)    -   b. nt-7620 A-to-G silent mutation (in bold)

                         NCR-57-T, D2 PDK-53 attenuation locus (wt D2 16681:C) >5′-Noncoding Region                                                                            >C         10        20        30        40        50        60        70        80        90       100 AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAATGTAGTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGA                                                                                                 M  N        110       120       130       140       150       160       170       180       190       200 ATAACCAACGGAAAAAGGCGAAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACT   N  Q  R  K  K  A  K  N  T  P  F  N  M  L  K  R  E  R  N  R  V  S  T  V  Q  Q  L  T  K  R  F  S  L        210       220       230       240       250       260       270       280       290       300 TGGAATGCTGCAGGGACGAGGACCATTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGGAGGGATATTGAAGAGA  G  M  L  Q  G  R  G  P  L  K  L  F  M  A  L  V  A  F  L  R  F  L  T  T  P  P  T  A  G  I  L  K  R        310       320       330       340       350       360       370       380       390       400 TGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAATAGGAGACGCAGATCTG W  G  T  I  K  K  S  K  A  I  N  V  L  R  G  E  R  K  E  T  G  R  M  L  N  T  L  N  R  R  R  R  S  A                                       >prM             Beginning of D3 16562 sequence        410       420       430       440       450      |460       470       480       490       500 CAGGCATGATCATTATGCTGATTCCAACAGTGATGGCGTTCCATTTAACCACGCGTGATGGAGAGCCGCGCATGATTGTGGGGAAGAATGAAAGAGGAAA   G  M  I  I  M  L  I  P  T  V  M  A  F  H  L  T  T  R  D  G  E  P  R  M  I  V  G  K  N  E  R  G  K                                                     |                                   Engineered MluI splicing site (nt-453 A-to-G silent mutation)        510       520       530       540       550       560       570       580       590       600 ATCCCTACTTTTCAAGACAGCCTCTGGAATCAACATGTGCACACTCATAGCTATGGATCTGGGAGAGATGTGTGATGACACGGTCACTTACAAATGCCCC  S  L  L  E  K  T  A  S  G  I  N  M  C  T  L  I  A  M  D  L  G  E  M  C  D  D  T  V  T  Y  K  C  P                                                    |                                                  Silent C-to-T nt mutation as clone marker        610       620       630       640       650       660       670       680       690       700 CACATTACCGAAGTGGAGCCTGAAGACATTGACTGCTGGTGCAACCTTACATCGACATGGGTGACTTATGGAACATGCAATCAAGCTGGAGAGCATAGAC H  I  T  E  V  E  P  E  D  I  D  C  W  C  N  L  T  S  T  W  V  T  Y  G  T  C  N  Q  A  G  E  H  R  R            > M        710       720       730       740       750       760       770       780       790       800 GCGATAAGAGATCAGTGGCGTTAGCTCCCCATGTTGGCATGGGACTGGACACACGCACTCAAACCTGGATGTCGGCTGAAGGAGCTTGGAGACAAGTCGA   D  K  R  S  V  A  L  A  P  H  V  G  M  G  L  D  T  R  T  Q  T  W  M  S  A  E  G  A  W  R  Q  V  E        810       820       830       840       850       860       870       880       890       900 GAAGGTAGAGACATGGGCCCTTAGGCACCCAGGGTTTACCATACTAGCCCTATTTCTTGCCCATTACATAGGCACTTCCTTGACCCAGAAAGTGGTTATT  K  V  E  T  W  A  L  R  H  P  G  F  T  I  L  A  L  F  L  A  H  Y  I  G  T  S  L  T  Q  K  V  V  I                                     > E        910       920       930       940       950       960       970       980       990      1000 TTTATACTATTAATGCTGGTTACCCCATCCATGACAATGAGATGTGTAGGAGTAGGAAACAGAGATTTTGTGGAAGGCCTATCGGGAGCTACGTGGGTTG F  I  L  L  M  L  V  T  P  S  M  T  M  R  C  V  G  V  G  N  R  D  F  V  E  G  L  S  G  A  T  W  V  D       1010      1020      1030      1040      1050      1060      1070      1080      1090      1100 ACGTGGTGCTCGAGCACGGTGGGTGTGTGACTACCATGGCTAAGAACAAGCCCACGCTGGACATAGAGCTTCAGAAGACCGAGGCCACCCAACTGGCGAC   V  V  L  E  H  G  G  C  V  T  T  M  A  K  N  K  P  T  L  D  I  E  L  Q  K  T  E  A  T  Q  L  A  T       1110      1120      1130      1140      1150      1160      1170      1180      1190      1200 CCTAAGGAAGCTATGCATTGAGGGAAAAATTACCAACATAACAACCGACTCAAGATGTCCCACCCAAGGGGAAGCGATTTTACCTGAGGAGCAGGACCAG  L  R  K  L  C  I  E  G  K  I  T  N  I  T  T  D  S  R  C  P  T  Q  G  E  A  I  L  P  E  E  Q  D  Q       1210      1220      1230      1240      1250      1260      1270      1280      1290      1300 AACTACGTGTGTAAGCATACATACGTGGACAGAGGCTGGGGAAACGGTTGTGGTTTGTTTGGCAAGGGAAGCTTGGTGACATGCGCGAAATTTCAATGTT N  Y  V  C  K  H  T  Y  V  D  R  G  W  G  N  G  C  G  L  F  G  K  G  S  L  V  T  C  A  K  F  Q  C  L       1310      1320      1330      1340      1350      1360      1370      1380      1390      1400 TAGAATCAATAGAGGGAAAAGTGGTGCAACATGAGAACCTCAAATACACCGTCATCATCACAGTGCACACAGGAGACCAACACCAGGTGGGAAATGAAAC   E  S  I  E  G  K  V  V  Q  H  E  N  L  K  Y  T  V  I  I  T  V  H  T  G  D  Q  H  Q  V  G  N  E  T       1410      1420      1430      1440      1450      1460      1470      1480      1490      1500 GCAGGGAGTCACGGCTGAGATAACACCCCAGGCATCAACCGCTGAAGCCATTTTACCTGAATATGGAACCCTCGGGCTAGAATGCTCACCACGGACAGGT  Q  G  V  T  A  E  I  T  P  Q  A  S  T  A  E  A  I  L  P  E   Y  G  T  L  G  L  E  C  S  P  R  T  G       1510      1520      1530      1540      1550      1560      1570      1580      1590      1600 TTGGATTTCAATGAAATGATCTCATTGACAATGAAGAACAAAGCATGGATGGTACATAGACAATGGTTCTTTGACTTACCCCTACCATGGACATCAGGAG L  D  F  N  E  M  I  S  L  T  M  K  N  K  A  W  M  V  H  R  Q  W  F  F  D  L  P  L  P  W  T  S  G  A       1610      1620      1630      1640      1650      1660      1670      1680      1690      1700 CTTCAGGAGAAACACCAACTTGGAACAGGAAAGAGCTTCTTGTGACATTTAAAAATGCACATGCAAAAAAGCAAGAAGTAGTTGTTCTTGGATCACAAGA   S  A  E  T  P  T  W  N  R  K  E  L  L  V  T  F  K  N  A  H  A  K  K  Q  E  V  V  V  L  G  S  Q  E   |Additional E-233 Thr-to-Ser mutation (wt D3 16562: nt-1603 A) in master and pre-master seed       1710      1720      1730      1740      1750      1760      1770      1780      1790      1800 GGGAGCAATGCATACAGCACTGACAGGAGCTACAGAGATCCAAACCTCAGGAGGCACAAGTATCTTTGCGGGGCACTTAAAATGTAGACTCAAGATGGAC  G  A  M  H  T  A  L  T  G  A  T  E  I  Q  T  S  G  G  T  S  I  F  A  G  H  L  K  C  R  L  K  M  D       1810      1820      1830      1840      1850      1860      1870      1880      1890      1900 AAATTGGAACTCAAGGGGATGAGCTATGCAATGTGCTTGAGTAGCTTTGTGTTGAAGAAAGAAGTCTCCGAAACGCAGCATGGGACAATACTCATTAAGG K  L  E  L  K  G  M  S  K  A  M  C  L  S  S  F  V  L  K  K  E  V  S  E  T  Q  H  G  T  I  L  I  K  V       1910      1920      1930      1940      1950      1960      1970      1980      1990      2000 TTGAGTACAAAGGGGAAGATGCACCCTGCAAGATTCCTTTCTCCACGGAGGATGGACAAGGAAAAGCTCTCAATGGCAGACTGATCACAGCCAATCCAGT   E  K  K  G  E  D  A  P  C  K  I  P  F  S  T  E  D  G  Q  G  K  A  L  N  G  R  L  I  T  A  N  P  V                                                                     |                           Engineered E-345 His-to-Leu (wt D3 16562: nt-1970-A) for efficient growth       2010      2020      2030      2040      2050      2060      2070      2080      2090      2100 GGTGACCAAGAAGGAGGAGCCTGTCAACATTGAGGCTGAACCTCCTTTTGGAGAAAGTAACATAGTAATTGGAATTGGAGACAAAGCCCTGAAAATCAAC  V  T  K  K  E  E  P  V  N  I  E  A  E  P  P  F  G  E  S  N  I  V  I  G  I  G  D  K  A  L  K  I  N       2110      2120      2130      2140      2150      2160      2170      2180      2190      2200 TGGTACAAGAAGGGAAGCTCGATTGGGAAGATGTTCGAGGCCACTGCCAGAGGTGCAAGGCGCATGGCCATCTTGGGAGACACAGCCTGGGACTTTGGAT W  Y  K  K  G  S  S  I  G  K  M  F  E  A  T  A  R  G  A  R  R  M  A  I  L  G  D  T  A  W  D  E  G  S       2210      2220      2230      2240      2250      2260      2270      2280      2290      2300 CAGTGGGTGGTGTTTTGAATTCATTAGGGAAAATGGTCCACCAAATATTTGGGAGTGCTTACACAGCCCTATTTGGTGGAGTCTCCTGGATGATGAAAAT   V  G  G  V  L  N  S  L  G  K  M  V  H  Q  I  E  G  S  A  Y  T  A  L  F  G  G  V  S  W  M  M  K  I                                                                  End of D3 16562 sequence       2310      2320      2330      2340      2350      2360      2370  |   2380      2390      2400 TGGAATAGGTGTCCTCTTAACCTGGATAGGGTTGAACTCAAAAAATACTTCTATGTCATTTTCATGCATCGCGGCCGGCATTGTGACACTGTATTTGGGA  G  I  G  V  L  L  T  W  I  G  L  N  S  K  N  T  S  M  S  F  S  C  I  A  A  G  I  V  T  L  Y  L  G                                                                        |                            Engineered NgoMIV splicing site, E-480 Val-to-Ala (nt-2375/2376 TG-to-CC)                > NS1       2410      2420      2430      2440      2450      2460      2470      2480      2490      2500 GTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGGA V  M  V  Q  A  D  S  G  C  V  V  S  W  K  N  K  E  L  K  C  G  S  G  I  F  I  T  D  N  V  H  T  W  T       2510     2520      2530      2540      2550      2560      2570      2580      2590      2600 CAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGRACATTTGTGGAATCCGCTCAGTAACAAG   E  Q  Y  K  F  Q  P  E  S  P  S  K  L  A  S  A  I  Q  K  A  H  E  E  D  I  C  G  I  R  S  V  T  R                                                                           |                                  D2 PDK-53 NS1-53-Asp atteniation locus (wt D2 16681: Gly, no-2573-G)      2610      2620      2630      2640      2650      2660      2670      2680      2690      2700 ACTGGAGAATCTGATGTGGAAACAAATAACACCAGAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATCAAAGGA  L  E  N  L  M  W  K  Q  I  T  P  E  L  N  H  I  L  S  E  N  E  V  K  L  T  I  M  T  G  D  I  K  G       2710      2720      2730      2740      2750      2760      2770      2780      2790      2800 ATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTATTCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAGAGTCTC I  M  Q  A  G  K  R  S  L  R  P  Q  P  T  E  L  K  Y  S  W  K  T  W  G  K  A  K  M  L  S  T  E  S  H       2810      2820      2830      2840      2850      2860      2870      2880      2890      2900 ATAACCAGACCTTTCTCATTGATGGCCCCGAAACAGGAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTGGAAGTTGAAGACTATGGCTTTGGAGT   N  Q  T  F  L  I  D  G  P  E  T  A  E  C  P  N  T  N  R  A  W  N  S  L  E  V  E  D  Y  G  E  G  V       2910      2920      2930      2940      2950      2960      2970      2980      2990      3000 ATTCACCACCAATATATGGCTAAAATTGAAAGAAAAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCCGTCCAT  F  T  T  N  I  W  L  K  L  K  E  K  Q  D  V  F  C  D  S  K  L  M  S  A  A  I  K  D  N  R  A  V  H       3010      3020      3030      3040      3050      3060      3070      3080      3090      3100 GCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAAAATCAC A  D  M  G  Y  W  I  E  S  A  L  N  D  T  W  K  I  E  K  A  S  F  I  E  V  K  N  C  H  W  P  K  S  H       3110      3120      3130      3140      3150      3160      3170      3180      3190      3200 ACACCCTCTGGAGCAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAACACAACTATAGACCAGGCTACCATAC   T  L  W  S  N  G  V  L  E  S  E  M  I  I  P  K  N  L  A  G  P  V  S  Q  H  N  Y  R  P  G  Y  H  T       3210      3220      3230      3240      3250      3260      3270      3280      3290      3300 ACAAATAACAGGACCATGGCATCTAGGTAAGCTTGAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAATAGAGGA  Q  I  T  G  P  W  H  L  G  K  L  E  M  D  F  D  F  C  D  G  T  T  V  V  V  T  E  D  C  G  N  R  G       3310      3320      3330      3340      3350      3360      3370      3380      3390      3400 CCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGGATGGGT P  S  L  R  T  T  T  A  S  G  K  L  I  T  E  W  C  C  R  S  C  T  L  P  P  L  R  Y  R  G  E  D  G  C                                                                        >NS2A       3410      3420      3430      3440      3450      3460      3470      3480      3490      3500 GCTGGTACGGGATGGAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGACATGGGCAGGTCGACAACTTTTCACT   W  Y  G  M  E  I  R  P  L  K  E  K  E  E  N  L  V  N  S  L  V  T  A  G  H  G  Q  V  D  N  F  S  L       3510      3520      3530      3540      3550      3560      3570      3580      3590      3600 AGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAAATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTGACATTG  G  V  L  G  M  A  L  F  L  E  E  M  L  R  T  R  V  G  T  K  H  A  I  L  L  V  A  V  S  F  V  T  L       3610      3620      3630      3640      3650      3660      3670      3680      3690      3700 ATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGCGCCACTATGACGGATGACATAGGTATGGGCGTGACTTATCTTGCCC I  T  G  N  M  S  F  R  D  L  G  R  V  M  V  M  V  G  A  T  M  T  D  D  I  G  M  G  V  T  Y  L  A  L       3710      3720      3730      3740      3750      3760      3770      3780      3790      3800 TACTAGCAGCCTTCAAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAAGGAATTGATGATGACTACTATAGGAATTGTACT   L  A  A  F  K  V  R  P  T  F  A  A  G  L  L  L  R  K  L  T  S  K  E  L  M  M  T  T  I  G  I  V  L       3810      3820      3830      3840      3850      3860      3870      3880      3890      3900 CCTCTCCCAGAGCACCATACCAGAGACCATTCTTGAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAAAAGTAT  L  S  Q  S  T  I  P  E  T  I  L  E  L  T  D  A  L  A  L  G  M  M  V  L  K  M  V  R  N  M  E  K  Y       3910      3920      3930      3940      3950      3960      3970      3980      3990      4000 CAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTACAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGGTGTCCG Q  L  A  V  T  I  M  A  I  L  C  V  P  N  A  V  I  L  Q  N  A  W  K  V  S  C  T  I  L  A  V  V  S  V       4010      4020      4030      4040      4050      4060      4070      4080      4090      4100 TTTCCCCACTGTTCTTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCTATTTTTCTAACAAC   S  P  L  F  L  T  S  S  Q  Q  K  T  D  W  I  P  L  A  L  T  I  K  G  L  N  P  T  A  I  F  L  T  T            |       D2 PDK-53 specific NS2A-181-Phe (wt D2 16681: Leu, nt-4012-C)                          > NS2B       4110      4120      4130      4140      4150      4160      4170      4180      4190      4200 CCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCATTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAAAATGAT  L  S  R  T  S  K  K  R  S  W  P  L  N  E  A  I  M  A  V  G  M  V  S  I  L  A  S  S  L  L  K  N  D       4210      4220      4230      4240      4250      4260      4270      4280      4290      4300 ATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAGCCGATG I  P  M  T  G  P  L  V  A  G  G  L  L  T  V  C  Y  V  L  T  G  R  S  A  D  L  E  L  E  R  A  A  D  V       4310      4320      4330      4340      4350      4360      4370      4380      4390      4400 TCAAATGGGAAGACCAGGCAGAGATATCAGGAAGGAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAATGAAGAGGAAGA   K  W  E  D  Q  A  E  I  S  G  S  S  P  I  L  S  I  T  I  S  E  D  G  S  M  S  I  K  N  E  E  E  E       4410      4420      4430      4440      4450      4460      4470      4480      4490      4500 ACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGGAGCATGGTACCTGTGGGAA  Q  T  L  T  I  L  I  R  T  G  L  L  V  I  S  G  L  F  P  V  S  I  P  I  T  A  A  A  W  Y  L  W  E                > NS3       4510      4520      4530      4540      4550      4560      4570      4580      4590      4600 GTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGCAAAAAG V  K  K  Q  R  A  G  V  L  W  D  V  P  S  P  P  P  M  G  K  A  E  L  E  D  G  A  Y  R  I  K  Q  K  G       4610      4620     4630      4640      4650      4660      4670      4680      4690      4700 GGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACACGTGGCGCTGTTCTAATGCATAAAGG   I  L  G  Y  S  Q  I  G  A  G  V  Y  K  E  G  T  F  H  T  M  W  H  V  T  R  G  A  V  L  M  H  K  G       4710      4720      4730      4740      4750      4760      4770      4780      4790      4800 AAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAAGAAGTC  K  R  I  E  P  S  W  A  D  V  K  K  D  L  I  S  Y  G  G  G  W  K  L  E  G  E  W  K  E  G  E  E  V       4810      4820      4830      4840      4850      4860      4870      4880      4890      4900 CAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCTGGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTATCTCTGG Q  V  L  A  L  E  P  G  K  N  P  R  A  V  Q  T  K  P  G  L  F  K  T  N  A  G  T  I  G  A  V  S  L  D       4910      4920      4930      4940      4950      4960      4970      4980      4990      5000 ACTTTTCTCCTGGAACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGTGTTGTTACAAGGAGTGGAGCATATGT   F  S  P  G  T  S  G  S  P  I  I  D  K  K  G  K  V  V  G  L  Y  G  N  G  V  V  T  R  S  G  A  Y  V       5010      5020      5030      5040      5050     5060      5070      5080      5090      5100 GAGTGCTATAGCCCAGACTGAAAAAAGCATTGAAGACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTCCACCCA  S  A  I  A  Q  T  E  K  S  I  E  D  N  P  E  I  E  D  D  I  F  R  K  R  R  L  T  I  M  D  L  H  P       5110      5120      5130      5140      5150      5160      5170      5180      5190      5200 GGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAACGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTGTGGCAG G  A  G  K  T  K  R  Y  L  P  A  I  V  R  E  A  I  K  R  G  L  R  T  L  I  L  A  P  T  R  V  V  A  A       5210      5220      5230      5240      5250      5260      5270      5280      5290      5300 CTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGTGCACACCGGGCGGGAGATTGTGGACCTAATGTGTCA   E  M  E  E  A  L  R  G  L  P  I  R  Y  Q  T  P  A  I  R  A  V  H  T  G  R  E  I  V  D  L  M  C  H                                                               |                           D2 PDK-53 NS3-250Val attenuation locus (D2 16681: Glu, nt-5270-A)      5310      5320      5330      5340      5350      5360      5370      5380      5390      5400 TGCCACATTTACCATGAGGCTGCTATCACCAGTTAGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGACCCAGCAAGTATAGCA  A  T  F  T  M  R  L  L  S  P  V  R  V  P  N  Y  N  L  I  I  M  D  E  A  H  F  T  D  P  A  S  I  A       5410      5420      5430      5440      5450      5460      5470      5480      5490      5500 GCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTTATGACAGCCACTCCCCCGGGAAGGAGAGACCCATTTCCTCAGAGCA A  R  G  Y  I  S  T  R  V  E  M  G  E  A  A  G  I  F  M  T  A  T  P  P  G  S  R  D  P  F  P  Q  S  N       5510      5520      5530      5540      5550      5560      5570      5580      5590      5600 ATGCACCAATCATAGATGAAGAAAGAGAAATCCCTGAACGCTCGTGGAATTCCGGACATGAATGGGTCACGGATTTTAAAGGGAAGACTGTTTGGTTCGT   A  P  I  I  D  E  E  R  E  I  P  E  R  S  W  N  S  G  H  E  W  V  T  D  F  K  G  K  T  V  W  F  V                                         |                                    D2 PDK-53 silent mutation nt-5541-C (D2 16681: T)       5610      5620      5630      5640      5650      5660      5670      5680      5690      5700 TCCAAGTATAAAAGGAGGAAATGATATAGGAGCTTGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAGTATGTC  P  S  I  K  A  G  N  D  I  A  A  C  L  R  K  N  G  K  K  V  I  Q  L  S  R  K  T  E  D  S  E  Y  V       5710      5720      5730      5740      5750      5760      5770      5780      5790      5800 AAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATGGGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGACGCTGCA K  T  R  T  N  D  W  D  F  V  V  T  T  D  I  S  E  M  G  A  N  F  K  A  E  R  V  I  D  P  R  R  C  M       5810      5820      5830      5840      5850      5860      5870      5880      5890      5900 TGAAACCAGTCATACTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAGAATAGG   K  P  V  I  L  T  D  G  E  E  R  V  I  L  A  G  P  M  P  V  T  H  S  S  A  A  Q  R  R  G  R  I  G       5910      5920      5930      5940      5950      5960      5970      5980      5990      6000 AAGAAATCCAAAAAATGAGAATGACCAGTACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATGCTCCTA  R  N  P  K  N  E  N  D  Q  Y  I  Y  M  G  E  P  L  E  N  D  E  D  C  A  H  W  K  E  A  K  M  L  L          6010      6020      6030      6040      6050      6060      6070      6080      6090      6100 GATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGTGAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAGGAGAAG D  N  I  N  T  P  E  G  I  I  P  S  M  F  E  P  E  R  E  K  V  D  A  I  D  G  E  Y  R  L  R  G  E  A       6110      6120      6130      6140      6150      6160      6170      6180      6190      6200 CAAGGAAAACCTTTGTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAAGGCATCAACTACGCAGACAGAAGGTG   R  K  T  F  V  D  L  M  R  R  G  D  L  P  V  W  L  A  Y  R  V  A  A  E  G  I  N  Y  A  D  R  R  W       6210      6220      6230      6240      6250      6260      6270      6280      6290      6300 GTGTTTTGATGGAGTCAAGAACAACCAAATCCTAGAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCCAGATGG  C  F  D  G  V  K  N  N  Q  I  L  E  E  N  V  E  V  E  I  W  T  K  E  G  E  R  K  K  L  K  P  R  W                                                                      >NS4A       6310      6320      6330      6340      6350      6360      6370      6380      6390      6400 TTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTTGCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAGAAATGG L  D  A  R  I  Y  S  D  P  L  A  L  K  E  E  K  E  F  A  A  G  R  K  S  L  T  L  N  L  I  T  E  M  G       6410      6420      6430      6440      6450      6460      6470      6480      6490      6500 GTAGGCTCCCAACCTTCATGACTCAGAAGGCAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAGGCAGGTGGAAGGGCGTACAACCATGC   R  L  P  T  F  M  T  Q  K  A  R  D  A  L  D  N  L  A  V  L  H  T  A  E  A  G  G  R  A  Y  N  H  A       6510      6520      6530      6540      6550      6560      6570      6580      6590      6600 TCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGCAAGGGGC  L  S  E  L  P  E  T  L  E  T  L  L  L  L  T  L  L  A  T  V  T  G  G  I  F  L  F  L  M  S  A  R  G                                                                                            |                                      D2 PDK-53 specific NS4A-75-A1a (wt D2 16681: Gly, nt-6599-G)       6610      6620      6630      6640      6650      6660      6670      6680      6690      6700 ATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTATGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAATAATAC I  G  K  M  T  L  G  M  C  C  I  I  T  A  S  I  L  L  W  Y  A  Q  I  Q  P  H  W  I  A  A  S  I  I  L       6710      6720      6730      6740      6750      6760      6770      6780      6790      6800 TGGAGTTTTTTCTCATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACCTACGTTGTCATAGCCATCCTCACAGT   E  F  F  L  I  V  L  L  I  P  E  P  E  K  Q  R  T  P  Q  D  N  Q  L  T  Y  V  V  I  A  T  L  T  V                    > NS4B       6810      6820      6830      6840      6850      6860      6870      6880      6890      6900 GGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGCAACATC  V  A  A  T  M  A  N  E  M  G  F  L  E  K  T  K  K  D  L  G  L  G  S  I  A  T  Q  Q  P  E  S  N  I       6910      6920      6930      6940      6950      6960      6970      6980      6990      7000 CTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATTCCTCAG L  D  I  D  L  R  P  A  S  A  W  T  L  Y  A  V  A  T  T  F  V  T  P  M  L  R  H  S  I  E  N  S  S  V       7010      7020      7030      7040      7050      7060      7070      7080      7090      7100 TGAATGTGTCCCTAACAGCTATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCCCCTTCT   N  V  S  L  T  A  I  A  N  Q  A  T  V  L  M  G  L  G  K  G  W  P  L  S  K  M  D  I  G  V  P  L  L       7110      7120      7130      7140      7150      7160      7170      7180      7190      7200 CGCCATTGGATGCTACTCACAAGTCAACCCCATAACTCTCACAGGAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTCCAAGCA  A  I  G  C  Y  S  Q  V  N  P  I  T  L  T  A  A  L  F  L  L  V  A  H  Y  A  I  I  G  P  G  L  Q  A       7210      7220      7230      7240      7250      7260      7270      7280      7290      7300 AAAGCAACCAGAGAAGCTCAGAAAAGAGGAGCGGCGGGCATCATGAAAAACCCAACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATACCTTATG K  A  T  R  E  A  Q  K  R  A  A  A  G  I  M  K  N  P  T  V  D  G  I  T  V  I  D  L  D  P  I  P  Y  D       7310      7320      7330      7340      7350      7360      7370      7380      7390      7400 ATCCAAAGTTTGAAAAGGAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTT   P  K  F  E  K  Q  L  G  Q  V  M  L  L  V  L  C  V  T  Q  V  L  M  M  R  T  T  W  A  L  C  E  A  L       7410      7420      7430      7440      7450      7460      7470      7480      7490      7500 AACCTTAGCTACCGGGCCCATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTTAGAGGG  T  L  A  T  G  P  I  S  T  L  W  E  G  N  P  G  R  F  W  N  T  T  I  A  V  S  M  A  N  I  E  R  G                                                                > NS5       7510      7520      7530      7540      7550      7560      7570      7580      7590      7600 AGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAACACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAAT S  Y  L  A  G  A  G  L  L  F  S  I  M  K  N  T  T  N  T  R  R  G  T  G  N  I  G  E  T  L  G  E  K  W       7610      7620      7630      7640      7650      7660      7670      7680      7690      7700 GGAAAAGCCGATTGAACGCGTTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGATAGAACCTTAGCAAAAGAAGGCATTAA   K  S  R  L  N  A  L  G  K  S  E  F  Q  I  Y  K  K  S  G  I  Q  E  V  D  R  T  L  A  K  E  G  I  K                    |            Additional nt-7260 A-to-G silent mutation in master and pre-master seeds       7710      7720      7730      7740      7750      7760      7770      7780      7790      7800 AAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTAGTGGAC  R  G  E  T  D  H  H  A  V  S  R  G  S  A  K  L  R  W  F  V  E  R  N  M  V  T  P  E  G  K  V  V  D       7810      7820      7830      7840      7850      7860      7870      7880      7890      7900 CTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACGAAGAAC L  G  C  G  R  G  G  W  S  Y  Y  C  G  G  L  K  N  V  R  E  V  K  G  L  T  K  G  G  P  G  H  E  E  P       7910      7920      7930      7940      7950      7960      7970      7980      7990      8000 CCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCAGAAAAGTGTGACACATTATTGTGTGA   I  P  M  S  T  Y  G  W  N  L  V  R  L  Q  S  G  V  D  V  F  F  I  P  P  E  K  C  D  T  L  L  C  D       8010      8020      8030      8040      8050      8060      8070      8080      8090      8100 CATAGGGGAGTCATCACCAAATCCCACAGTGGAAGGAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAATTTTGC  I  G  E  S  S  P  N  P  T  V  E  A  G  R  T  L  R  V  L  N  L  V  E  N  W  L  N  N  N  T  Q  F  C       8110      8120      8130      8140      8150      8160      8170      8180      8190      8200 ATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCTCACGAA I  K  V  L  N  P  Y  M  P  S  V  I  E  K  M  E  A  L  Q  R  K  Y  G  G  A  L  V  R  N  P  L  S  R  N       8210      8220      8230      8240      8250      8260      8270      8280      8290      8300 ACTCCACACATGAGATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATCAACAGATTTACAATGAG   S  T  H  E  M  Y  W  V  S  N  A  S  G  N  I  V  S  S  V  N  M  I  S  R  M  L  I  N  R  F  T  M  R       8310      8320      8330      8340      8350      8360      8370      8380      8390      8400 ATACAAGAAAGCCACTTACGAGCCGGATGTTGACCTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATTGGGAAA  Y  K  K  A  T  Y  E  P  D  V  D  L  G  S  G  T  R  N  I  G  I  E  S  E  I  P  N  L  D  I  I  G  K       8410      8420      8430      8440      8450      8460      8470      8480      8490      8500 AGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGACCACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAACAAAAC R  I  E  K  I  K  Q  E  H  E  T  S  W  H  Y  D  Q  D  H  P  Y  K  T  W  A  Y  H  G  S  Y  E  T  K  Q       8510      8520      8530      8540      8550      8560      8570      8580      8590      8600 AGACTGGATCAGCATCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATGGTGACACAGATGGCAATGACAGACAC   T  G  S  A  S  S  M  V  N  G  V  V  R  L  L  T  K  P  W  D  V  V  P  M  V  T  Q  M  A  M  T  D  T       8610      8620      8630      8640      8650      8660      8670      8680      8690      8700 GACTCCATTTGGACAACAGCGCGTTTTTAAAGAGAAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACAGGAGAG  T  P  F  G  Q  Q  R  V  F  K  E  K  V  D  T  R  T  Q  E  P  K  E  G  T  K  K  L  M  K  I  T  A  E       8710      8720      8730      8740      8750      8760      8770      8780      8790      8800 TGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAAGAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGGCCATAT W  L  W  K  E  L  G  K  K  K  T  P  R  M  C  T  R  E  E  F  T  R  K  V  R  S  N  A  A  L  G  A  I  F       8810      8820      8830      8840      8850      8860      8870      8880      8890      8900 TCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGAAGGAAA   T  D  E  N  K  W  K  S  A  R  E  A  V  E  D  S  R  F  W  E  L  V  D  K  E  R  N  L  H  L  E  G  K       8910      8920      8930      8940      8950      8960      8970      8980      8990      9000 GTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGGAGAGCCATATGGTACATGTGGCTT  C  E  T  C  V  Y  N  M  M  G  K  R  E  K  K  L  G  E  F  G  K  A  K  G  S  R  A  I  W  Y  M  W  L       9010      9020      9030      9040      9050      9060      9070      9080      9090      9100 GGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAGGGCTGC G  A  R  F  L  E  F  E  A  L  G  F  L  N  E  D  H  W  F  S  R  E  N  S  L  S  G  V  E  G  E  G  L  H       9110      9120      9130      9140      9150      9160      9170      9180      9190      9200 ACAAGCTAGGTTACATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGATGGGATACAAGAATCACACTAGAAGA   K  L  G  Y  I  L  R  D  V  S  K  K  E  G  G  A  M  Y  A  D  D  T  A  G  W  D  T  R  I  T  L  E  D       9210      9220      9230      9240      9250      9260      9270      9280      9290      9300 CCTAAAAAATGAAGAAATGGTAACAAACCACATGGAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTGGTGCGT  L  K  N  E  E  M  V  T  N  H  M  E  G  E  H  K  K  L  A  E  A  I  F  K  L  T  Y  Q  N  K  V  V  R       9310      9320      9330      9340      9350      9360      9370      9380      9390      9400 GTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATACTTTCA V  Q  R  P  T  P  R  G  T  V  M  D  I  I  S  R  R  D  Q  R  G  S  G  Q  V  G  T  Y  G  L  N  T  F  T       9410      9420      9430      9440      9450      9460      9470      9480      9490      9500 CCAATATGGAAGCCCAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATCACAGAAGAAATCGCTGTGCAAAACTG  N  M  E  A  Q  L  I  R  Q  M  E  G  E  G  V  E  K  S  I  Q  H  L  T  I  T  E  E  I  A  V  Q  N  W       9510      9520      9530      9540      9550      9560      9570      9580      9590      9600 GTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCTTTAACA  L  A  R  V  G  R  E  R  L  S  R  M  A  I  S  G  D  D  C  V  V  K  P  L  D  D  R  F  A  S  A  L  T       9610      9620      9630      9640      9650      9660      9670      9680      9690      9700 GCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCAAGAGGATGGAAtgATTGGACACAAGTGCCCTTCTGTTCACACCATTA  L  N  D  M  G  K  I  R  K  D  I  Q  Q  W  E  P  S  R  G  W  N  D  W  T  Q  V  P  F  C  S  H  H  F       9710      9720      9730      9740      9750      9760      9770      9780      9790      9800 TCCATGAGTTAATCATGAAAGACGGTCGCGTACTCGTTGTTCCATGTAGAAACCAAGATGAACTGATTGGCAGAGCCCGAATCTCCCAAGGAGGAGGGTG   H  E  L  I  M  K  D  G  R  V  L  V  V  P  C  R  N  Q  D  E  L  I  G  R  A  R  I  S  Q  G  A  G  W       9810      9820      9830      9840      9850      9860      9870      9880      9890      9900 GTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAATGCTATT  S  L  R  E  T  A  C  L  G  K  S  Y  A  Q  M  W  S  L  M  Y  F  H  R  R  D  L  R  L  A  A  N  A  F       9910      9920      9930      9940      9950      9960      9970      9980      9990 10000 TGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATACATGCTAAACATGAATGGATGACAACGGAAGACATGCTGACAGTCT G  S  A  V  P  S  H  W  V  P  T  S  R  T  T  W  S  I  H  A  K  H  E  W  M  T  T  E  D  M  L  T  V  W      10010     10020     10030     10040     10050     10060     10070     10080     10090     10100 GGAACAGGGTGTGGATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACTTGGGGAAAAGAGAAGACCAATG   N  R  V  W  I  Q  E  N  P  W  M  E  D  K  T  P  V  E  S  W  E  E  T  P  Y  L  G  K  R  E  D  Q  W      10110     10120     10130     10140     10150     10160     10170     10180     10190     10200 GTGCGGCTCATTGATTGGGTTAACAAGGAGGGCCACCTGGGCAAAGAACATCCAAGGAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAAGAATAC  C  G  S  L  I  G  L  T  S  R  A  T  W  A  K  N  I  Q  A  A  T  N  Q  V  R  S  L  I  G  N  E  E  Y                                                                >3′-Noncoding Region      10210     10220     10230     10240     10250     10260     10270     10280     10290     10300 ACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGGAGGAGTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTAGAAGTC T  D  Y  M  P  S  M  K  R  F  R  R  E  E  E  E  A  G  V  L  W  *       10310     10320     10330     10340     10350     10360     10370     10380     10390     10400 AGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCATAAATGCCATAGCTTGAG      10410     10420     10430     10440     10450     10460     10470     10480     10490     10500 TAAACTATGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGCGTAGTGGACTAGCGGTTAG      10510     10520     10530     10540     10550     10560     10570     10580     10590     10600 AGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGAAGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGACCCCCCC      10610     10620     10630     10640     10650     10660     10670     10680     10690     10700 GAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGAATGGTGCTG      10710  TTGAATCAACAGGTTCT 

DENvax-4 Master Virus Seed (MVS)

Nucleotide sequence of the chimeric viral genome and deduced amino acidsequence of the translated protein. Most of the prM-E gene (nt-457 to-2379, underlined) is wild-type (wt) DEN-4 1036 virus-specific; theremaining nucleotide sequence is DEN-2 PDK-53 virus-specific. Allengineered substitutions differ from wt virus (DEN-3 16562 or DEN-216681), as well as extra mutations (changes from engineered cDNA clone)are marked.

Substitutions Included in the Genome and Protein:

Junction sites:

-   -   a. MluI (nt 451-456): engineered silent mutation, nt-453 A-to-G    -   b. NgoMIV (nt 2380-2385): engineered mutations, nt-2381/2382        TG-to-CC (resulted in E-482 Val-to-Ala change)

D2 PDK-53 virus backbone (change from wt D2 16681)

-   -   a. 5′-noncoding region(NCR)-57 (nt-57 C-to-T): major attenuation        locus (in red)    -   b. NS1-53 Gly-to-Asp (nt-2579 G-to-A): major attenuation locus        (in red)    -   c. NS2A-181 Leu-to-Phe (nt-4018 C-to-T, in bold)    -   d. NS3-250 Glu-to-Val (nt-5270 A-to-T): major attenuation locus        (in red)    -   e. nt-5547 (NS3 gene) T-to-C silent mutation (in bold)    -   f. NS4A-75 Gly-to-Ala (nt-6599 G-to-C, in bold)    -   * nt-8571 C-to-T silent mutation of PDK-53 is not engineered in        the vaccine virus

Engineered substitutions in cDNA clone

-   -   a. Engineered C-100 Arg-to-Ser (nt-396 A-to-C): may improve        viral replication in culture    -   b. Engineered nt-1401 A-to-G silent mutation    -   c. Engineered E-364 Ala-to-Val (nt-2027 C-to-T): may improve        viral replication in culture    -   d. Engineered E-447 Met-to-Leu (nt-2275 A-to-C): may improve        viral replication in culture

Additional substitutions found in vaccine seed (0.06% nt different fromoriginal clone)

-   -   a. nt-225 (C gene) A-to-T silent mutation (in bold)    -   b. NS2A-66 Asp-to-Gly (nt-3674 A-to-G) mutation (in bold)    -   c. NS2A-99 Lys-to-Lys/Arg mix (nt-3773 A-to-A/G mix, in bold)    -   d. nt-5391 C-to-T (NS3 gene) silent mutation (in bold)    -   e. NS4A-21 Ala-to-Val (nt-6437 C-to-T, in bold)    -   f. nt-7026 T-to-C/T mix silent mutation (in bold)    -   g. nt-9750 A-to-C silent mutation (in bold)

                                        NCR-57-T, D2 PDK-53 attenuation locus (wt D2 16681: C) >5′-Noncoding Region                                    |                                     >C         10        20        30        40        50        60        70        80        90       100 AGTTGTTAGTCTACGTGGACCGACAAAGACAGATTCTTTGAGGGAGCTAAGCTCAATGTAGTTCTAACAGTTTTTTAATTAGAGAGCAGATCTCTGATGA                                                                                                 M  N        110       120       130       140       150       160       170       180       190       200 ATAACCAACGGAAAAAGGCGAAAAACACGCCTTTCAATATGCTGAAACGCGAGAGAAACCGCGTGTCGACTGTGCAACAGCTGACAAAGAGATTCTCACT   N  Q  R  K  K  A  K  N  T  P  F  N  M  L  K  R  E  R  N  R  V  S  T  V  Q  Q  L  T  K  R  F  S  L        210       220       230       240       250       260       270       280       290       300 TGGAATGCTGCAGGGACGAGGACCTTTAAAACTGTTCATGGCCCTGGTGGCGTTCCTTCGTTTCCTAACAATCCCACCAACAGCAGGGATATTGAAGAGA  G  M  L  Q  G  R  G  P  L  K  L  F  M  A  L  V  A  F  L  R  F  L  T  I  P  P  T  A  G  I  L  K  R                         |                     Additional nt-225 A-to-T silent mutation in master and pre-master seeds        310       320       330       340       350       360       370       380       390       400 TGGGGAACAATTAAAAAATCAAAAGCTATTAATGTTTTGAGAGGGTTCAGGAAAGAGATTGGAAGGATGCTGAACATCTTGAATAGGAGACGCAGCTCTG W  G  T  I  K  K  S  K  A  I  N  V  L  R  G  F  R  K  E  I  G  R  M  L  N  I  L  N  R  R  R  S  S  A                                                                                              |                                                          Engineered C-100 Arg-to-Ser (nt 396 A-to-C)                                       >prM            Beginning of D4 1036 sequence        410       420       430       440       450      |460       470       480       490       500 CAGGCATGATCATTATGCTGATTCCAACAGTGATGGCGTTCCATTTAACCACGCGTGATGGCGAACCCCTCATGATAGTGGCAAAACATGAAAGGGGGAG   G  M  I  I  M  L  I  P  T  V  M  A  F  H  L  T  T  R  D  G  E  P  L  M  I  V  A  K  H  E  R  G  R                                                     |                                           Engineered MluI splicing site (nt-453 A-to-G silent)        510       520       530       540       550       560       570       580       590       600 ACCTCTCTTGTTTAAGACAACAGAGGGGATCAACAAATGCACTCTCATTGCCATGGACTTGGGTGAAATGTGTGAGGACACTGTCACGTATAAATGCCCC  P  L  L  F  K  T  T  E  G  I  N  K  C  T  L  I  A  M  D  L  G  E  M  C  E  D  T  V  T  Y  K  C  P        610       620       630       640       650       660       670       680       690       700 TTACTGGTCAATACCGAACCTGAAGACATTGATTGCTGGTGCAATCTCACGTCTACCTGGGTCATGTATGGGACATGCACCCAGAGCGGAGAACGGAGAC L  L  V  N  T  E  P  E  D  I  D  C  W  C  N  L  T  S  T  W  V  M  Y  G  T  C  T  Q  S  G  E  R  R  R            > M        710       720       730       740       750       760       770       780       790       800 GAGAGAAGCGCTCAGTAGCTTTAACACCACATTCAGGAATGGGATTGGAAACAAGAGCTGAGACATGGATGTCATCGGAAGGGGCTTGGAAGCATGCTCA   E  K  R  S  V  A  L  T  P  H  S  G  M  G  L  E  T  R  A  E  T  W  M  S  S  E  G  A  W  K  H  A  Q        810       820       830       840       850       860       870       880       890       900 GAGAGTAGAGAGCTGGATACTCAGAAACCCAGGATTCGCGCTCTTGGCAGGATTTATGGCTTATATGATTGGGCAAACAGGAATCCAGCGAACTGTCTTC  R  V  E  S  W  I  L  R  N  P  G  F  A  L  L  A  G  F  M  A  Y  M  I  G  Q  T  G  I  Q  R  T  V  F                                     > E        910       920       930       940       950       960       970       980       990      1000 TTTGTCCTAATGATGCTGGTCGCCCCATCCTACGGAATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCG F  V  L  M  M  L  V  A  P  S  Y  G  M  R  C  V  G  V  G  N  R  D  F  V  E  G  V  S  G  G  A  W  V  D       1010      1020      1030      1040      1050      1060      1070      1080      1090      1100 ATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCT   L  V  L  E  H  G  G  C  V  T  T  M  A  Q  G  K  P  T  L  D  F  E  L  T  K  T  T  A  K  E  V  A  L       1110      1120      1130      1140      1150      1160      1170      1180      1190      1200 GTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTAAAAGAGGAACAAGACCAA  L  R  T  Y  C  I  E  A  S  I  S  N  I  T  T  A  T  R  C  P  T  Q  G  E  P  Y  L  K  E  E  Q  D  Q       1210      1220      1230      1240      1250      1260      1270      1280      1290      1300 CAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTT Q  Y  I  C  R  R  D  V  V  D  R  G  W  G  N  G  C  G  L  F  G  K  G  G  V  V  T  C  A  K  F  S  C  S       1310      1320      1330      1340      1350      1360      1370      1380      1390      1400 CGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACAC   G  K  I  T  G  N  L  V  Q  I  E  N  L  E  Y  T  V  V  V  T  V  H  N  G  D  T  H  A  V  G  N  D  T       1410      1420      1430      1440      1450      1460      1470      1480      1490      1500 GTCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGG  S  N  H  G  V  T  A  T  I  T  P  R  S  P  S  V  E  V  K  L  P  D  Y  G  E  L  T  L  D  C  E  P  R | Silent nt-1401 A-to-G mutation in engineered clone       1510      1520      1530      1540      1550      1560      1570      1580      1590      1600 TCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTTGTGCATAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAG S  G  I  D  F  N  E  M  I  L  M  K  M  K  K  K  T  W  L  V  H  K  Q  W  F  L  D  L  P  L  P  W  T  A       1610      1620      1630      1640      1650      1660      1670      1680      1690      1700 CAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATC   G  A  D  T  S  E  V  H  W  N  Y  K  E  R  M  V  T  F  K  V  P  H  A  K  R  Q  D  V  T  V  L  G  S       1710      1720      1730      1740      1750      1760      1770      1780      1790      1800 TCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGT  Q  E  G  A  M  H  S  A  L  A  G  A  T  E  V  D  S  G  D  G  N  H  M  F  A  G  H  L  K  C  K  V  R       1810      1820      1830      1840      1850      1860      1870      1880      1890      1900 ATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGG M  E  K  L  R  I  K  G  M  S  Y  T  M  C  S  G  K  F  S  I  D  K  E  M  A  E  T  C  H  G  T  T  V  V       1910      1920      1930      1940 1950      1960      1970      1980      1990      2000 TGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCAC   K  V  K  Y  E  G  A  G  A  P  C  K  V  P  I  E  I  R  D  V  N  K  E  K  V  V  G  R  I  I  S  S  T       2010      2020      2030      2040      2050      2060      2070      2080      2090      2100 CCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAGTTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGTGCATTAACA  P  L  A  E  N  T  N  S  V  T  N  I  E  L  E  P  P  F  G  D  S  Y  T  V  T  G  V  G  N  S  A  L  T                          |             Engineered E-364 Ala-to-Val (nt-2027 C-to-T) to improve viral growth in culture       2110      2120      2130      2140      2150      2160      2170      2180      2190      2200 CTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATT L  H  W  F  R  K  G  S  S  I  G  K  M  F  E  S  T  Y  R  G  A  K  R  M  A  T  L  G  E  T  A  W  D  F       2210      2220      2230      2240      2250      2260      2270      2280      2290      2300 TTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCCTGTTTGGAGGAGTCTCATGGATGAT   G  S  V  G  G  L  F  T  S  L  G  K  A  V  H  Q  V  F  G  S  V  Y  T  T  L  F  G  G  V  S  W  M  I                                                                           |                                             Engineered E-447 Met-to-Leu (nt-2275 A-to-C) mutation                                                         End of D4 1036 sequence       2310      2320      2330      2340      2350      2360      2370        |      2390      2400 TAGAATCCTAATTGGGTTCCTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGCCGGCATTGTGACACTGTAT  R  I  L  I  G  F  L  V  L  W  I  G  T  N  S  R  N  T  S  M  A  M  T  C  I  A  A  G  I  V  T  L  Y                                                                                |                            Engineered NgoMIV splicing site, E-482 Val-to-Ala (nt-2381/2382 TG-to-CC)                      > NS1       2410      2420      2430      2440      2450      2460      2470      2480      2490      2500 TTGGGGGTCATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAATGTGGCAGTGGGATTTTCATCACAGACAACGTGCACA L  G  V  M  V  Q  A  D  S  G  C  V  V  S  W  K  N  K  E  L  K  C  G  S  G  I  F  I  T  D  N  V  H  T       2510      2520      2530      2540      2550      2560      2570      2580      2590      2600 CATGGACAGAACAATACAAGTTCCAACCAGAATCCCCTTCAAAACTAGCTTCAGCTATCCAGAAAGCCCATGAAGAGGACATTTGTGGAATCCGCTCAGT   W  T  E  Q  Y  K  F  Q  P  E  S  P  S  K  L  A  S  A  I  Q  K  A  H  E  E  D  I  C  G  I  R  S  V                                                                              |                              D2 PDK-53 NS1-53-Asp attenuation locus (wt D2 16681: Gly, no-2579-G)      2610      2620      2630      2640      2650      2660      2670      2680      2690      2700 AACAAGACTGGAGAATCTGATGTGGAAACAAATAACACCAGAATTGAATCACATTCTATCAGAAAATGAGGTGAAGTTAACTATTATGACAGGAGACATC  T  R  L  E  N  L  M  W  K  Q  I  T  P  E  L  N  H  I  L  S  E  N  E  V  K  L  T  I  M  T  G  D  T       2710      2720      2730      2740      2750      2760      2770      2780      2790      2800 AAAGGAATCATGCAGGCAGGAAAACGATCTCTGCGGCCTCAGCCCACTGAGCTGAAGTATTCATGGAAAACATGGGGCAAAGCAAAAATGCTCTCTACAG K  G  I  M  C  A  G  K  R  S  L  R  P  Q  P  T  E  L  K  Y  S  W  K  T  W  G  K  A  K  M  L  S  T  E       2810      2820      2830      2840      2850      2860      2870      2880      2890      2900 AGTCTCATAACCAGACCTTTCTCATTGATGGCCCCGAAACAGGAGAATGCCCCAACACAAATAGAGCTTGGAATTCGTTGGAAGTTGAAGACTATGGCTT   S  H  N  Q  T  F  L  I  D  G  P  E  T  A  E  C  P  N  T  N  R  A  W  N  S  L  E  V  E  D  Y  G  F       2910      2920      2930      2940      2950      2960      2970      2980      2990      3000 TGGAGTATTCACCACCAATATATGGCTAAAATTGAAAGAAAAACAGGATGTATTCTGCGACTCAAAACTCATGTCAGCGGCCATAAAAGACAACAGAGCC  G  V  F  T  T  N  I  W  L  K  L  K  E  K  Q  D  V  F  C  D  S  K  L  M  S  A  A  I  K  D  N  R  A       3010      3020      3030      3040      3050      3060      3070      3080      3090      3100 GTCCATGCCGATATGGGTTATTGGATAGAAAGTGCACTCAATGACACATGGAAGATAGAGAAAGCCTCTTTCATTGAAGTTAAAAACTGCCACTGGCCAA V  H  A  D  M  G  Y  W  I  E  S  A  L  N  D  T  W  K  I  E  K  A  S  F  I  E  V  K  N  C  H  W  P  K       3110      3120      3130      3140      3150      3160      3170      3180      3190      3200 AATCACACACCCTCTGGAGCAATGGAGTGCTAGAAAGTGAGATGATAATTCCAAAGAATCTCGCTGGACCAGTGTCTCAACACAACTATAGACCAGGCTA   S  H  T  L  W  S  N  G  V  L  E  S  E  M  I  I  P  K  N  L  A  G  P  V  S  C  H  N  Y  R  P  G  Y       3210      3220      3230      3240      3250      3260      3270      3280      3290      3300 CCATACACAAATAACAGGACCATGGCATCTAGGTAAGCTTGAGATGGACTTTGATTTCTGTGATGGAACAACAGTGGTAGTGACTGAGGACTGCGGAAAT  H  T  Q  I  I  G  P  W  H  L  G  K  L  E  M  D  F  D  F  C  C  G  T  T  V  V  V  T  E  D  C  G  N       3310      3320      3330      3340      3350      3360      3370      3380      3390      3400 AGAGGACCCTCTTTGAGAACAACCACTGCCTCTGGAAAACTCATAACAGAATGGTGCTGCCGATCTTGCACATTACCACCGCTAAGATACAGAGGTGAGG R  G  P  S  L  R  T  T  T  A  S  G  K  L  I  T  E  W  C  C  R  S  C  T  L  P  P  L  R  Y  R  G  E  D                                                                             >NS2A       3410      3420      3430      3440      3450      3460      3470      3480      3490      3500 ATGGGTGCTGGTACGGGATGGAAATCAGACCATTGAAGGAGAAAGAAGAGAATTTGGTCAACTCCTTGGTCACAGCTGGACATGGGCAGGTCGACAACTT   G  C  W  Y  G  M  E  I  R  P  L  K  E  K  E  E  N  L  V  N  S  L  V  T  A  G  H  G  Q  V  D  N  F       3510      3520      3530      3540      3550      3560      3570      3580      3590      3600 TTCACTAGGAGTCTTGGGAATGGCATTGTTCCTGGAGGAAATGCTTAGGACCCGAGTAGGAACGAAACATGCAATACTACTAGTTGCAGTTTCTTTTGTG  S  L  G  V  L  G  M  A  L  F  L  E  E  M  L  R  T  R  V  G  T  K  H  A  I  L  L  V  A  V  S  F  V       3610      3620      3630      3640      3650      3660      3670      3680      3690      3700 ACATTGATCACAGGGAACATGTCCTTTAGAGACCTGGGAAGAGTGATGGTTATGGTAGGCGCCACTATGACGGGTGACATAGGTATGGGCGTGACTTATC T  L  I  T  G  N  M  S  F  R  D  L  G  R  V  M  V  M  V  G  A  T  M  T  G  D  I  G  M  G  V  T  Y  L                                                                         |             Additional NS2A-66 Asp-to-Gly (nt-3674 A-to-G mutation) in master and pre-master seeds       3710      3720      3730      3740      3750      3760      3770      3780      3790      3800 TTGCCCTACTAGCAGCCTTCAAAGTCAGACCAACTTTTGCAGCTGGACTACTCTTGAGAAAGCTGACCTCCAGGGAATTGATGATGACTACTATAGGAAT   A  L  L  A  A  F  K  V  R  P  T  F  A  A  G  L  L  L  R  K  L  T  S  K  E  L  M  M  T  T  I  G  I                                                                        |                      Additional NS2A-99 K to R/K (mix) (nt-3773 A-to-G/A) mutation in master seed       3810      3820      3830      3840      3850      3860      3870      3880      3890      3900 TGTACTCCTCTCCCAGAGCACCATACCAGAGACCATTCTTGAGTTGACTGATGCGTTAGCCTTAGGCATGATGGTCCTCAAAATGGTGAGAAATATGGAA  V  L  L  S  Q  S  T  I  P  E  T  I  L  E  L  T  D  A  L  A  L  G  M  M  V  L  K  M  V  R  N  M  E       3910      3920      3930      3940      3950      3960      3970      3980      3990      4000 AAGTATCAATTGGCAGTGACTATCATGGCTATCTTGTGCGTCCCAAACGCAGTGATATTACAAAACGCATGGAAAGTGAGTTGCACAATATTGGCAGTGG K  Y  Q  L  A  V  T  I  M  A  I  L  C  V  P  N  A  V  I  L  Q  N  A  W  K  V  S  C  T  I  L  A  V  V       4010      4020      4030      4040      4050      4060      4070      4080      4090      4100 TGTCCGTTTCCCCACTGTTCTTAACATCCTCACAGCAAAAAACAGATTGGATACCATTAGCATTGACGATCAAAGGTCTCAATCCAACAGCTATTTTTCT   S  V  S  P  L  F  L  T  S  S  Q  Q  K  T  D  W  I  P  L  A  L  T  I  K  G  L  N  P  T  A  I  F  L                  | D2 PDK-53 specific NS2A-181-Phe (wt D2 16681: Leu, nt-4018-C)                                > NS2B       4110      4120      4130      4140      4150      4160      4170      4180      4190      4200 AACAACCCTCTCAAGAACCAGCAAGAAAAGGAGCTGGCCATTAAATGAGGCTATCATGGCAGTCGGGATGGTGAGCATTTTAGCCAGTTCTCTCCTAAAA  T  T  L  S  R  T  S  K  K  R  S  W  P  L  N  E  A  I  M  A  V  G  M  V  S  I  L  A  S  S  L  L  K       4210      4220      4230      4240      4250      4260      4270      4280      4290      4300 AATGATATTCCCATGACAGGACCATTAGTGGCTGGAGGGCTCCTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCAG N  D  I  P  M  T  G  P  L  V  A  G  G  L  L  T  V  C  Y  V  L  T  G  R  S  A  D  L  E  L  E  R  A  A       4310      4320      4330      4340      4350      4360      4370      4380     4390      4400 CCGATGTCAAATGGGAAGACCAGGCAGAGATATCAGGAAGGAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAATGAAGA   D  V  K  W  E  D  Q  A  E  I  S  G  S  S  P  I  L  S  I  T  I  S  E  D  G  S  M  S  I  K  N  E  E       4410      4420      4430      4440      4450      4460      4470      4480      4490      4500 GGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGGAGCATGGTACCTG  E  E  Q  T  L  T  I  L  T  R  T  G  L  L  V  I  S  G  L  F  P  V  S  I  P  I  T  A  A  A  W  Y  L                      > NS3       4510      4520      4530      4540      4550      4560      4570      4580      4590      4600 TGGGAAGTGAAGAAACAACGGGCCGGAGTATTGTGGGATGTTCCTTCACCCCCACCCATGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATTAAGC W  E  V  K  K  Q  R  A  G  V  L  W  D  V  P  S  P  P  P  M  G  K  A  E  L  E  D  G  A  Y  R  I  K  Q       4610      4620      4630      4640      4650      4660      4670      4680      4690      4700 AAAAAGGGATTCTTGGATATTCCCAGATCGGAGCCGGAGTTTACAAAGAAGGAACATTCCATACAATGTGGCATGTCACACGTGGCGCTGTTCTAATGCA   K  G  I  L  G  Y  S  Q  I  G  A  G  V  Y  K  E  G  T  F  H  T  M  W  H  V  T  R  G  A  V  L  M  H       4710      4720      4730      4740      4750      4760      4770      4780      4790      4800 TAAAGGAAAGAGGATTGAACCATCATGGGCGGACGTCAAGAAAGACCTAATATCATATGGAGGAGGCTGGAAGTTAGAAGGAGAATGGAAGGAAGGAGAA  K  G  K  R  I  E  P  S  W  A  D  V  K  K  D  L  I  S  Y  G  G  G  W  K  L  E  G  E  W  K  E  G  E       4810      4820      4830      4840      4850      4860      4870      4880      4890      4900 GAAGTCCAGGTATTGGCACTGGAGCCTGGAAAAAATCCAAGAGCCGTCCAAACGAAACCTGGTCTTTTCAAAACCAACGCCGGAACAATAGGTGCTGTAT E  V  Q  V  L  A  L  E  P  G  K  N  P  R  A  V  Q  T  K  P  G  L  F  K  T  N  A  G  T  I  G  A  V  S       4910      4920      4930      4940      4950      4960      4970      4980      4990      5000 CTCTGGACTTTTCTCCTGGAACGTCAGGATCTCCAATTATCGACAAAAAAGGAAAAGTTGTGGGTCTTTATGGTAATGGTGTTGTTACAAGGAGTGGAGC   L  D  F  S  P  G  T  S  G  S  P  I  I  D  K  K  G  K  V  V  G  L  Y  G  N  G  V  V  T  R  S  G  A       5010      5020      5030      5040      5050      5060      5070      5080      5090      5100 ATATGTGAGTGCTATAGCCCAGACTGAAAAAAGCATTGAAGACAACCCAGAGATCGAAGATGACATTTTCCGAAAGAGAAGACTGACCATCATGGACCTC  Y  V  S  A  I  A  Q  T  E  K  S  I  E  D  N  P  E  I  E  D  D  I  F  R  K  R  R  L  T  I  M  D  L       5110      5120      5130      5140      5150      5160      5170      5180      5190      5200 CACCCAGGAGCGGGAAAGACGAAGAGATACCTTCCGGCCATAGTCAGAGAAGCTATAAAACGGGGTTTGAGAACATTAATCTTGGCCCCCACTAGAGTTG H  P  G  A  G  K  T  K  R  Y  L  P  A  I  V  R  E  A  I  K  R  G  L  R  T  L  I  L  A  P  T  R  V  V       5210      5220      5230      5240      5250      5260      5270      5280      5290      5300 TGGCAGCTGAAATGGAGGAAGCCCTTAGAGGACTTCCAATAAGATACCAGACCCCAGCCATCAGAGCTGTGCACACCGGGCGGGAGATTGTGGACCTAAT   A  A  E  M  E  E  A  L  R  G  L  P  I  R  Y  Q  T  P  A  I  R  A  V  H  T  G  R  E  I  V  D  L  M                                                                     |                              D2 PDK-53 NS3-250-Val attenuation locus (D2 16681: Glu, nt-5270-A)      5310      5320      5330      5340      5350      5360      5370      5380      5390      5400 GTGTCATGCCACATTTACCATGAGGCTGCTATCACCAGTTAGAGTGCCAAACTACAACCTGATTATCATGGACGAAGCCCATTTCACAGATCCAGCAAGT  C  H  A  T  F  T  M  R  L  L  S  P  V  R  V  P  N  Y  N  L  I  I  M  D  E  A  H  F  T  D  P  A  S                                                                                           |                             Additional nt-5391 C-to-T silent mutation in mater and pre-master seeds       5410      5420      5430      5440      5450      5460      5470      5480      5490      5500 ATAGGAGCTAGAGGATACATCTCAACTCGAGTGGAGATGGGTGAGGCAGCTGGGATTTTTATGACAGCCACTCCCCCGGGAAGGAGAGACCCATTTCCTC I  A  A  R  G  Y  I  S  T  R  V  E  M  G  E  A  A  G  I  F  M  T  A  T  P  P  G  S  R  D  P  F  P  Q       5510      5520      5530      5540      5550      5560      5570      5580      5590      5600 AGAGCAATGCACCAATCATAGATGAAGAAAGAGAAATCCCTGAACGCTCGTGGAATTCCGGACATGAATGGGTCACGGATTTTAAAGGGAAGACTGTTTG   S  N  A  P  I  I  D  E  E  R  E  I  P  E  R  S  W  N  S  G  H  E  W  V  T  D  F  K  G  K  T  V  W                                               |                                    D2 PDK-53 specific silent mutation nt-5547-C (D2 16681: T)       5610      5620      5630      5640      5650      5660      5670      5680      5690      5700 GTTCGTTCCAAGTATAAAAGGAGGAAATGATATAGGAGCTTGCCTGAGGAAAAATGGAAAGAAAGTGATACAACTCAGTAGGAAGACCTTTGATTCTGAG  F  V  P  S  I  K  A  G  N  D  I  A  A  C  L  R  K  N  G  K  K  V  I  Q  L  S  R  K  T  F  D  S  E       5710      5720      5730      5740      5750      5760      5770      5780      5790      5800 TATGTCAAGACTAGAACCAATGATTGGGACTTCGTGGTTACAACTGACATTTCAGAAATGGGTGCCAATTTCAAGGCTGAGAGGGTTATAGACCCCAGAC Y  V  K  T  R  T  N  D  W  D  E  V  V  T  T  D  I  S  E  M  G  A  N  F  K  A  E  R  V  I  D  P  R  R       5810      5820      5830      5840      5850      5860      5870      5880      5890      5900 GCTGCATGAAACCAGTCATACTAACAGATGGTGAAGAGCGGGTGATTCTGGCAGGACCTATGCCAGTGACCCACTCTAGTGCAGCACAAAGAAGAGGGAG   C  M  K  P  V  I  L  T  D  G  E  E  R  V  I  L  A  G  P  M  P  V  T  H  S  S  A  A  Q  R  R  G  R       5910      5920      5930      5940      5950      5960      5970      5980      5990      6000 AATAGGAAGAAATCCAAAAAATGAGAATGACCAGTACATATACATGGGGGAACCTCTGGAAAATGATGAAGACTGTGCACACTGGAAAGAAGCTAAAATG  I  G  R  N  P  K  N  E  N  D  Q  Y  I  Y  M  G  E  P  L  E  N  D  E  D  C  A  H  W  K  E  A  K  M       6010      6020      6030      6040      6050      6060      6070      6080      6090      6100 CTCCTAGATAACATCAACACGCCAGAAGGAATCATTCCTAGCATGTTCGAACCAGAGCGTGAAAAGGTGGATGCCATTGATGGCGAATACCGCTTGAGAG L  L  D  N  I  N  T  P  E  G  I  I  P  S  M  F  E  P  E  R  E  K  V  D  A  I  D  G  E  Y  R  L  R  G       6110      6120      6130      6140      6150      6160      6170      6180      6190      6200 GAGAAGCAAGGAAAACCTTTGTAGACTTAATGAGAAGAGGAGACCTACCAGTCTGGTTGGCCTACAGAGTGGCAGCTGAAGGCATCAACTACGCAGACAG   E  A  R  K  T  F  V  D  L  M  R  R  G  D  L  P  V  W  L  A  Y  R  V  A  A  E  G  I  N  Y  A  D  R       6210      6220      6230      6240      6250      6260      6270      6280      6290      6300 AAGGTGGTGTTTTGATGGAGTCAAGAACAACCAAATCCTAGAAGAAAACGTGGAAGTTGAAATCTGGACAAAAGAAGGGGAAAGGAAGAAATTGAAACCC  R  W  C  F  D  G  V  K  N  N  Q  I  L  E  E  N  V  E  V  E  I  W  T  K  E  G  E  R  K  K  L  K  P                                                                            >NS4A       6310      6320      6330      6340      6350      6360      6370      6380      6390      6400 AGATGGTTGGATGCTAGGATCTATTCTGACCCACTGGCGCTAAAAGAATTTAAGGAATTTGCAGCCGGAAGAAAGTCTCTGACCCTGAACCTAATCACAG R  W  L  D  A  R  T  Y  S  D  P  L  A  L  K  E  F  K  E  F  A  A  G  R  K  S  L  T  L  N  L  I  T  E       6410      6420      6430      6440      6450      6460      6470      6480      6490      6500 AAATGGGTAGGCTCCCAACCTTCATGACTCAGAAGGTAAGAGACGCACTGGACAACTTAGCAGTGCTGCACACGGCTGAGGCAGGTGGAAGGGCGTACAA   M  G  R  L  P  T  F  M  T  Q  K  V  R  D  A  L  D  N  L  A  V  L  H  T  A  E  A  G  G  R  A  Y  N                                    |             Additional NS4A-21 Ala-to-Val (nt-6437 C-to-T) mutation in mater and pre-master seeds       6510      6520      6530      6540      6550      6560      6570      6580      6590      6600 CCATGCTCTCAGTGAACTGCCGGAGACCCTGGAGACATTGCTTTTACTGACACTTCTGGCTACAGTCACGGGAGGGATCTTTTTATTCTTGATGAGCGCA  H  A  L  S  E  L  P  E  T  L  E  T  L  L  L  L  T  L  L  A  T  V  T  G  G  I  F  L  F  L  M  S  A                                                                                                  |                                        D2 PDK-53 specific NS4A-75-Ala (wt D2 16681: Gly, nt-6599-G)       6610      6620      6630      6640      6650      6660      6670      6680      6690      6700 AGGGGCATAGGGAAGATGACCCTGGGAATGTGCTGCATAATCACGGCTAGCATCCTCCTATGGTACGCACAAATACAGCCACACTGGATAGCAGCTTCAA R  G  I  G  K  M  T  L  G  M  C  C  I  I  T  A  S  I  L  L  W  Y  A  Q  I  Q  P  H  W  I  A  A  S  T       6710      6720      6730      6740      6750      6760      6770      6780      6790      6800 TAATACTGGAGTTTTTTCTCATAGTTTTGCTTATTCCAGAACCTGAAAAACAGAGAACACCCCAAGACAACCAACTGACCTACGTTGTCATAGCCATCCT   I  L  E  F  F  L  I  V  L  L  I  P  E  P  E  K  Q  R  T  P  Q  D  N  Q  L  T  Y  V  V  I  A  I  L                          > NS4B       6810      6820      6830      6840      6850      6860      6870      6880      6890      6900 CACAGTGGTGGCCGCAACCATGGCAAACGAGATGGGTTTCCTAGAAAAAACGAAGAAAGATCTCGGATTGGGAAGCATTGCAACCCAGCAACCCGAGAGC  T  V  V  A  A  T  M  A  N  E  M  G  F  L  E  K  T  K  K  D  L  G  L  G  S  I  A  T  Q  Q  P  E  S       6910      6920      6930      6940      6950      6960      6970      6980      6990      7000 AACATCCTGGACATAGATCTACGTCCTGCATCAGCATGGACGCTGTATGCCGTGGCCACAACATTTGTTACACCAATGTTGAGACATAGCATTGAAAATT N  I  L  D  I  D  L  R  P  A  S  A  W  T  L  Y  A  V  A  T  T  F  V  T  P  M  L  R  H  S  I  E  N  S       7010      7020      7030      7040      7050      7060      7070      7080      7090      7100 CCTCAGTGAATGTGTCCCTAACAGCCATAGCCAACCAAGCCACAGTGTTAATGGGTCTCGGGAAAGGATGGCCATTGTCAAAGATGGACATCGGAGTTCC   S  V  N  V  S  L  T  A  I  A  N  Q  A  T  V  L  M  G  L  G  K  G  W  P  L  S  K  M  D  I  G  V  P                          |                    Additional nt-7026 T-to-C/T mix silent mutation in master and pre-master seeds       7110      7120      7130      7140      7150      7160      7170      7180      7190      7200 CCTTCTCGCCATTGGATGCTACTCACAAGTCAACCCCATAACTCTCACAGGAGCTCTTTTCTTATTGGTAGCACATTATGCCATCATAGGGCCAGGACTC  L  L  A  I  G  C  Y  S  Q  V  N  P  I  T  L  T  A  A  L  F  L  L  V  A  H  Y  A  I  I  G  P  G  L       7210      7220      7230      7240      7250      7260      7270      7280      7290      7300 CAAGCAAAAGCAACCAGAGAAGCTCAGAAAAGAGGAGCGGCGGGCATCATGAAAAACCCAACTGTCGATGGAATAACAGTGATTGACCTAGATCCAATAC Q  A  K  A  T  R  E  A  Q  K  R  A  A  A  G  I  M  K  N  P  T  V  D  G  I  T  V  I  D  L  D  P  I  P       7310      7320      7330      7340      7350      7360      7370      7380      7390      7400 CTTATGATCCAAAGTTTGAAAAGGAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGTGACTCAAGTATTGATGATGAGGACTACATGGGCTCTGTGTGA   Y  D  P  K  F  E  K  Q  L  G  Q  V  M  L  L  V  L  C  V  T  Q  V  L  M  M  R  T  T  W  A  L  C  E       7410      7420      7430      7440      7450      7460      7470      7480      7490      7500 GGCTTTAACCTTAGCTACCGGGCCCATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCGGTGTCAATGGCTAACATTTTT  A  L  T  L  A  T  G  P  I  S  T  L  W  E  G  N  P  G  R  F  W  N  T  T  I  A  V  S  M  A  N  I  F                                                                      >NS5       7510      7520      7530      7540      7550      7560      7570      7580      7590      7600 AGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCTATTATGAAGAACACAACCAACACAAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAG R  G  S  Y  L  A  G  A  G  L  L  F  S  I  M  K  N  T  T  N  T  R  R  G  T  G  N  I  G  E  T  L  G  E       7610      7620      7630      7640      7650      7660      7670      7680      7690      7700 AGAAATGGAAAAGCCGATTGAACGCATTGGGAAAAAGTGAATTCCAGATCTACAAGAAAAGTGGAATCCAGGAAGTGGATAGAACCTTAGCAAAAGAAGG   K  W  K  S  R  L  N  A  L  G  K  S  E  F  Q  I  Y  K  K  S  G  I  Q  E  V  D  R  T  L  A  K  E  G       7710      7720      7730      7740      7750      7760      7770      7780      7790      7800 CATTAAAAGAGGAGAAACGGACCATCACGCTGTGTCGCGAGGCTCAGCAAAACTGAGATGGTTCGTTGAGAGAAACATGGTCACACCAGAAGGGAAAGTA  I  K  R  G  E  T  D  H  H  A  V  S  R  G  S  A  K  L  R  W  F  V  E  R  N  M  V  T  P  E  G  K  V         7810      7820      7830      7840      7850      7860      7870      7880      7890      7900 GTGGACCTCGGTTGTGGCAGAGGAGGCTGGTCATACTATTGTGGAGGACTAAAGAATGTAAGAGAAGTCAAAGGCCTAACAAAAGGAGGACCAGGACACG V  D  L  G  C  G  R  G  G  W  S  Y  Y  C  G  G  L  K  N  V  R  E  V  K  G  L  T  K  G  G  P  G  H  E       7910      7920      7930      7940      7950      7960      7970      7980      7990      8000 AAGAACCCATCCCCATGTCAACATATGGGTGGAATCTAGTGCGTCTTCAAAGTGGAGTTGACGTTTTCTTCATCCCGCCAGAAAAGTGTGACACATTATT   E  P  I  P  M  S  T  Y  G  W  N  L  V  R  L  Q  S  G  V  D  V  F  F  I  P  P  E  K  C  D  T  L  L       8010      8020      8030      8040      8050      8060      8070      8080      8090      8100 GTGTGACATAGGGGAGTCATCACCAAATCCCACAGTGGAAGGAGGACGAACACTCAGAGTCCTTAACTTAGTAGAAAATTGGTTGAACAACAACACTCAA  C  D  I  G  E  S  S  P  N  P  T  V  E  A  G  R  T  L  R  V  L  N  L  V  E  N  W  L  N  N  N  T  Q       8110      8120      8130      8140      8150      8160      8170      8180      8190      8200 TTTTGCATAAAGGTTCTCAACCCATATATGCCCTCAGTCATAGAAAAAATGGAAGCACTACAAAGGAAATATGGAGGAGCCTTAGTGAGGAATCCACTCT F  C  I  K  V  L  N  P  Y  M  P  S  V  I  E  K  M  E  A  L  Q  R  K  Y  G  G  A  L  V  R  N  P  L  S       8210      8220      8230      8240      8250      8260      8270      8280      8290      8300 CACGAAACTCCACACATGAGATGTACTGGGTATCCAATGCTTCCGGGAACATAGTGTCATCAGTGAACATGATTTCAAGGATGTTGATCAACAGATTTAC   R  N  S  T  H  E  M  Y  W  V  S  N  A  S  G  N  I  V  S  S  V  N  M  I  S  R  M  L  I  N  R  F  T       8310      8320      8330      8340      8350      8360      8370      8380      8390      8400 AATGAGATACAAGAAAGCCACTTACGAGCCGGATGTTGACCTCGGAAGCGGAACCCGTAACATCGGGATTGAAAGTGAGATACCAAACCTAGATATAATT  M  R  Y  K  K  A  T  Y  E  P  D  V  D  L  G  S  G  T  R  N  I  G  I  E  S  E  I  P  N  L  D  I  I       8410      8420      8430      8440      8450      8460      8470      8480      8490      8500 GGGAAAAGAATAGAAAAAATAAAGCAAGAGCATGAAACATCATGGCACTATGACCAAGACCACCCATACAAAACGTGGGCATACCATGGTAGCTATGAAA G  K  R  I  E  K  I  K  Q  E  H  E  T  S  W  H  Y  D  Q  D  H  P  Y  K  T  W  A  Y  H  G  S  Y  E  T       8510      8520      8530      8540      8550      8560      8570      8580      8590      8600 CAAAACAGACTGGATCAGCATCATCCATGGTCAACGGAGTGGTCAGGCTGCTGACAAAACCTTGGGACGTCGTCCCCATGGTGACACAGATGGCAATGAC   K  Q  T  G  S  A  S  S  M  V  N  G  V  V  R  L  L  T  K  P  W  D  V  V  P  M  V  T  Q  M  A  M  T       8610      8620      8630      8640      8650      8660      8670      8680      8690      8700 AGACACGACTCCATTTGGACAACAGCGCGTTTTTAAAGAGAAAGTGGACACGAGAACCCAAGAACCGAAAGAAGGCACGAAGAAACTAATGAAAATAACA  D  T  T  P  F  G  Q  Q  R  V  F  K  E  K  V  D  T  R  T  Q  E  P  K  E  G  T  K  K  L  M  K  I  T       8710      8720      8730      8740      8750      8760      8770      8780      8790      8800 GCAGAGTGGCTTTGGAAAGAATTAGGGAAGAAAAAGACACCCAGGATGTGCACCAGAGAAGAATTCACAAGAAAGGTGAGAAGCAATGCAGCCTTGGGGG A  E  W  L  W  K  E  L  G  K  K  K  T  P  R  M  C  T  R  E  E  F  T  R  K  V  R  S  N  A  A  L  G  A       8810      8820      8830      8840      8850      8860      8870      8880      8890      8900 CCATATTCACTGATGAGAACAAGTGGAAGTCGGCACGTGAGGCTGTTGAAGATAGTAGGTTTTGGGAGCTGGTTGACAAGGAAAGGAATCTCCATCTTGA   I  F  T  D  E  N  K  W  K  S  A  R  E  A  V  E  D  S  R  F  W  E  L  V  D  K  E  R  N  L  H  L  E       8910      8920      8930      8940      8950      8960      8970      8980      8990      9000 AGGAAAGTGTGAAACATGTGTGTACAACATGATGGGAAAAAGAGAGAAGAAGCTAGGGGAATTCGGCAAGGCAAAAGGCAGGAGAGCCATATGGTACATG  G  K  C  E  T  C  V  Y  N  M  M  G  K  R  E  K  K  L  G  E  F  G  K  A  K  G  S  R  A  I  W  Y  M       9010      9020      9030      9040      9050      9060      9070      9080      9090      9100 TGGCTTGGAGCACGCTTCTTAGAGTTTGAAGCCCTAGGATTCTTAAATGAAGATCACTGGTTCTCCAGAGAGAACTCCCTGAGTGGAGTGGAAGGAGAAG W  L  G  A  R  F  L  E  F  E  A  L  G  E  L  N  E  D  H  W  F  S  R  E  N  S  L  S  G  V  E  G  E  G       9110      9120      9130      9140      9150      9160      9170      9180      9190      9200 GGCTGCACAAGCTAGGTTACATTCTAAGAGACGTGAGCAAGAAAGAGGGAGGAGCAATGTATGCCGATGACACCGCAGGATGGGATACAAGAATCACACT   L  H  K  L  G  Y  I  L  R  D  V  S  K  K  E  G  G  A  M  Y  A  D  D  T  A  G  W  D  T  R  I  T  L        9210      9220      9230      9240      9250      9260      9270      9280      9290      9300 AGAAGACCTAAAAAATGAAGAAATGGTAACAAACCACATGGAAGGAGAACACAAGAAACTAGCCGAGGCCATTTTCAAACTAACGTACCAAAACAAGGTG  E  D  L  K  N  E  E  M  V  T  N  H  M  E  G  E  H  K  K  L  A  E  A  I  F  K  L  T  Y  Q  N  K  V       9310      9320      9330      9340      9350      9360      9370      9380      9390      9400 GTGCGTGTGCAAAGACCAACACCAAGAGGCACAGTAATGGACATCATATCGAGAAGAGACCAAAGAGGTAGTGGACAAGTTGGCACCTATGGACTCAATA V  R  V  Q  R  P  T  P  R  G  T  V  M  D  T  T  S  R  R  D  Q  R  G  S  G  Q  V  G  T  Y  G  L  N  T       9410      9420      9430      9440      9450      9460      9470      9480      9490      9500 CTTTCACCAATATGGAAGCCCAACTAATCAGACAGATGGAGGGAGAAGGAGTCTTTAAAAGCATTCAGCACCTAACAATCACAGAAGAAATCGCTGTGCA   F  T  N  M  E A  Q  L  I  R  Q  M  E  G  E  G  V  E  K  S  I  Q  H  L  T  I  T  E  E  I  A  V  Q       9510      9520      9530      9540      9550      9560      9570      9580      9590      9600 AAACTGGTTAGCAAGAGTGGGGCGCGAAAGGTTATCAAGAATGGCCATCAGTGGAGATGATTGTGTTGTGAAACCTTTAGATGACAGGTTCGCAAGCGCT  N  W  L  A  R  V  G  R  E  R  L  S  R  M  A  I  S  G  D  D  C  V  V  K  P  L  D  D  R  F  A  S  A       9610      9620      9630      9640      9650      9660      9670      9680      9690      9700 TTAACAGCTCTAAATGACATGGGAAAGATTAGGAAAGACATACAACAATGGGAACCTTCAAGAGGATGGAATGATTGGACACAAGTGCCCTTCTGTTCAC L  T  A  L  N  D  M  G  K  I  R  K  D  I  Q  Q  W  E  P  S  R  G  W  N  D  W  T  Q  V  P  F  C  S  H       9710      9720      9730      9740      9750      9760      9770      9780      9790      9800 ACCATTTCCATGAGTTAATCATGAAAGACGGTCGCGTACTCGTTGTTCCCTGTAGAAACCAAGATGAACTGATTGGCAGAGCCCGAATCTCCCAAGGAGC   H  F  H  E  L  I  M  K  D  G  R  V  L  V  V  P  C  R  N  Q  D  E  L  I  G  R  A  R  I  S  Q  G  A                                                  |                           Additional nt-9750 A-to-C silent mutation in master and pre-master seeds       9810      9820      9830      9840      9850      9860      9870      9880      9890      9900 AGGGTGGTCTTTGCGGGAGACGGCCTGTTTGGGGAAGTCTTACGCCCAAATGTGGAGCTTGATGTACTTCCACAGACGCGACCTCAGGCTGGCGGCAAAT G  W  S  L  R  E  T  A  C  L  G  K  S  Y  A  Q  M  W  S  L  M  Y  F  H  R  R  D  L  R  L  A  A  N       9910      9920      9930      9940      9950      9960      9970      9980      9990     10000 GCTATTTGCTCGGCAGTACCATCACATTGGGTTCCAACAAGTCGAACAACCTGGTCCATACATGCTAAACATGAATGGATGACAACGGAAGACATGCTGA A  I  C  S  A  V  P  S  H  W  V  P  T  S  R  T  T  W  S  I  H  A  K  H  E  W  M  T  T  E  D  M  L  T      10010     10020     10030     10040     10050     10060     10070     10080     10090     10100 CAGTCTGGAACAGGGTGTGGATTCAAGAAAACCCATGGATGGAAGACAAAACTCCAGTGGAATCATGGGAGGAAATCCCATACTTGGGGAAAAGAGAAGA   V  W  N  R  V  W  I  Q  E  N  P  W  M  E  D  K  T  P  V  E  S  W  E  E  T  P  Y  L  G  K  R  E  D      10110     10120     10130     10140     10150     10160     10170     10180     10190     10200 CCAATGGTGCGGCTCATTGATTGGGTTAACAAGGAGGGCCACCTGGGCAAAGAACATCCAAGGAGCAATAAATCAAGTTAGATCCCTTATAGGCAATGAA  Q  W  C  G  S  L  I  G  L  T  S  R  A  T  W  A  K  N  I  Q  A  A  I  N  Q  V  R  S  L  I  G  N  E                                                                        >3′-Noncoding Region      10210     10220     10230     10240     10250     10260     10270     10280     10290     10300 GAATACACAGATTACATGCCATCCATGAAAAGATTCAGAAGAGAAGAGGAAGAAGGAGGAGTTCTGTGGTAGAAAGCAAAACTAACATGAAACAAGGCTA E  Y  T  D  Y  M  P  S  M  K  R  F  R  R  E  E  E  E  A  G  V  L  W  *      10310     10320     10330     10340     10350     10360     10370     10380     10390     10400 GAAGTCAGGTCGGATTAAGCCATAGTACGGAAAAAACTATGCTACCTGTGAGCCCCGTCCAAGGACGTTAAAAGAAGTCAGGCCATCATAAATGCCATAG      10410     10120     10430    10440     10450     10460     10470     10480     10490     10400CTTGAGTAAACTATGCAGCCTGTAGCTCCACCTGAGAAGGTGTAAAAAATCCGGGAGGCCACAAACCATGGAAGCTGTACGCATGGGCGTAGTGGACTAG     10510     10520     10530     10540     10550     10560     10570     10580     10590     10600GGTTAGAGGAGACCCCTCCCTTACAAATCGCAGCAACAATGGGGGCCCAAGGCGAGATGAAGCTGTAGTCTCGCTGGAAGGACTAGAGGTTAGAGGAGAC     10610     10620    10630         10640     10650     10660     10670     10680     10690     10700CCCCCCCGAAACAAAAAACAGCATATTGACGCTGGGAAAGACCAGAGATCCTGCTGTCTCCTCAGCATCATTCCAGGCACAGAACGCCAGAAAATGGATG     10710     10720 GTGCTGTTGAATCAACAGGTTCT

What is claimed:
 1. A nucleic acid sequence comprising a nucleic acidsequence encoding a modified live, attenuated dengue-2 virus representedby SEQ ID NO:13 (WVS).
 2. A pharmaceutical composition comprising thenucleic acid sequence according to claim 1, and a pharmaceuticallyacceptable excipient.
 3. A method for inducing an immune response in asubject comprising, administering the pharmaceutical composition ofclaim 2 to the subject, wherein the composition induces an immuneresponse in the subject against at least one dengue virus serotype.
 4. Avector comprising a nucleic acid sequence according to claim
 1. 5. Thepharmaceutical composition according to claim 2, further comprising oneor more live, attenuated dengue viruses having a nucleotide sequenceencoding a dengue virus or dengue virus chimera represented by SEQ IDNOS: 1, 3, 5, and 7, which is a dengue-1/dengue-2 chimera.
 6. Thepharmaceutical composition according to claim 2, wherein the compositioncontains at least one, live attenuated dengue virus that represents eachof the four dengue virus serotypes, wherein the composition is atetravalent composition.
 7. The pharmaceutical composition according toclaim 2, further comprising an immunogenic composition comprising alive, attenuated flavivirus selected from the group consisting of yellowfever virus, tick-borne encephalitis virus, Japanese encephalitis virus,West Nile virus, hepatitis C virus and a combination of two or morethereof.
 8. A method for inducing an immune response in a subjectcomprising, administering the pharmaceutical composition of claim 5 tothe subject, wherein the composition induces an immune response in thesubject against at least one dengue virus serotype.
 9. The methodcomposition according to claim 8, wherein the composition contains atleast one, live attenuated dengue virus that represents each of the fourdengue virus serotypes, wherein the composition is a tetravalentcomposition.
 10. A kit comprising the immunogenic composition accordingto claim 5, and a container.
 11. A dengue-2 nucleic acid sequencerepresented by SEQ ID NO: 13 encoding species containing nucleotide G orC at nucleotide position
 6481. 12. A dengue-2 nucleic acid sequencerepresented by SEQ ID NO:13 encoding species containing nucleotide C orT at nucleotide position
 7156. 13. An isolated cell comprising at leastone of the nucleic acid sequences according to claim
 1. 14. A method formanufacturing a pharmaceutical composition comprising, combining atleast one of the nucleic acid sequences according to claim 1 and apharmaceutically acceptable excipient and making a pharmaceuticallyacceptable composition for use in inducing an immune response againstdengue virus in a subject.